Species-specific, genus-specific and universal DNA probes and amplification primers to rapidly detect and identify common bacterial and fungal pathogens and associated antibiotic resistance genes from clinical specimens for diagnosis in microbiology laboratories

ABSTRACT

DNA-based methods employing amplification primers or probes for detecting, identifying, and quantifying in a test sample DNA from (i) any bacterium, (ii) the species  Streptococcus agalactiae, Staphylococcus saprophyticus, Enterococcus faecium, Neisseria meningitidis, Listeria monocytogenes  and  Candida albicans , and (iii) any species of the genera Streptococcus, Staphylococcus, Enterococcus, Neisseria and Candida are disclosed. DNA-based methods employing amplification primers or probes for detecting, identifying, and quantifying in a test sample antibiotic resistance genes selected from the group consisting of bla tem , bla rob , bla shv , bla oxa , blaZ, aadB, aacC1, aacC2, aacC3, aacA4, aac6′-lla, ermA, ermB, ermC, mecA, vanA, vanB, vanC, satA, aac(6′)-aph(2″), aad(6′), vat, vga, msrA, sul and int are also disclosed. The above microbial species, genera and resistance genes are all clinically relevant and commonly encountered in a variety of clinical specimens. These DNA-based assays are rapid, accurate and can be used in clinical microbiology laboratories for routine diagnosis. These novel diagnostic tools should be useful to improve the speed and accuracy of diagnosis of microbial infections, thereby allowing more effective treatments. Diagnostic kits for (i) the universal detection and quantification of bacteria, and/or (ii) the detection, identification and quantification of the above-mentioned bacterial and fungal species and/or genera, and/or (iii) the detection, identification and quantification of the above-mentioned antibiotic resistance genes are also claimed.

BACKGROUND OF THE INVENTION

[0001] Classical Methods for the Identification and Susceptibility Testing of Bacteria

[0002] Bacteria are classically identified by their ability to utilize different substrates as a source of carbon and nitrogen through the use of biochemical tests such as the API20E™ system (bioMérieux). For susceptibility testing, clinical microbiology laboratories use methods including disk diffusion, agar dilution and broth microdilution. Although identifications based on biochemical tests and antibacterial susceptibility tests are cost-effective, at least two days are required to obtain preliminary results due to the necessity of two successive overnight incubations to identify the bacteria from clinical specimens as well as to determine their susceptibility to antimicrobial agents. There are some commercially available automated systems (i.e. the MicroScan system from Dade Diagnostics Corp. and the Vitek system from bioMerieux) which use sophisticated and expensive apparatus for faster microbial identification and susceptibility testing (Stager and Davis, 1992, Clin. Microbiol. Rev. 5:302-327). These systems require shorter incubation periods, thereby allowing most bacterial identifications and susceptibility testing to be performed in less than 6 hours. Nevertheless, these faster systems always require the primary isolation of the bacteria as a pure culture, a process which takes at least 18 hours for a pure culture or 2 days for a mixed culture. The fastest identification system, the autoSCAN-Walk-Away™ system (Dade Diagnostics Corp.) identifies both gram-negative and gram-positive bacterial species from standardized inoculum in as little as 2 hours and gives susceptibility patterns to most antibiotics in 5.5 hours. However, this system has a particularly high percentage (i.e. 3.3 to 40.5%) of non-conclusive identifications with bacterial species other than Enterobacteriaceae (Croizé J., 1995, Lett. Infectiol. 10:109-113; York et al., 1992, J. Clin. Microbiol. 30:2903-2910). For Enterobacteriaceae, the percentage of non-conclusive identifications was 2.7 to 11.4%.

[0003] A wide variety of bacteria and fungi are routinely isolated and identified from clinical specimens in microbiology laboratories. Tables 1 and 2 give the incidence for the most commonly isolated bacterial and fungal pathogens from various types of clinical specimens. These pathogens are the most frequently associated with nosocomial and community-acquired human infections and are therefore considered the most clinically important.

[0004] Clinical Specimens Tested in Clinical Microbiology Laboratories

[0005] Most clinical specimens received in clinical microbiology laboratories are urine and blood samples. At the microbiology laboratory of the Centre Hospitalier de l'UniversitéLaval (CHUL), urine and blood account for approximately 55% and 30% of the specimens received, respectively (Table 3). The remaining 15% of clinical specimens comprise various biological fluids including sputum, pus, cerebrospinal fluid, synovial fluid, and others (Table 3). Infections of the urinary tract, the respiratory tract and the bloodstream are usually of bacterial etiology and require antimicrobial therapy. In fact, all clinical samples received in the clinical microbiology laboratory are tested routinely for the identification of bacteria and susceptibility testing.

[0006] Conventional Pathogen Identification from Clinical Specimens

[0007] Urine Specimens

[0008] The search for pathogens in urine specimens is so preponderant in the routine microbiology laboratory that a myriad of tests have been developed. However, the gold standard remains the classical semi-quantitative plate culture method in which 1 μL of urine is streaked on plates and incubated for 18-24 hours. Colonies are then counted to determine the total number of colony forming units (CFU) per liter of urine. A bacterial urinary tract infection (UTI) is normally associated with a bacterial count of 10⁷ CFU/L or more in urine. However, infections with less than 10⁷ CFU/L in urine are possible, particularly in patients with a high incidence of diseases or those catheterized (Stark and Maki, 1984, N. Engl. J. Med. 311:560-564). Importantly, approximately 80% of urine specimens tested in clinical microbiology laboratories are considered negative (i.e. bacterial count of less than 10⁷ CFU/L; Table 3). Urine specimens found positive by culture are further characterized using standard biochemical tests to identify the bacterial pathogen and are also tested for susceptibility to antibiotics. The biochemical and susceptibility testing normally require 18-24 hours of incubation.

[0009] Accurate and rapid urine screening methods for bacterial pathogens would allow a faster identification of negative specimens and a more efficient treatment and care management of patients. Several rapid identification methods (Uriscreen™, UTIscreen™, Flash Track™ DNA probes and others) have been compared to slower standard biochemical methods, which are based on culture of the bacterial pathogens. Although much faster, these rapid tests showed low sensitivities and poor specificities as well as a high number of false negative and false positive results (Koening et al., 1992, J. Clin. Microbiol. 30:342-345; Pezzlo et al., 1992, J. Clin. Microbiol. 30:640-684).

[0010] Blood Specimens

[0011] The blood specimens received in the microbiology laboratory are always submitted for culture. Blood culture systems may be manual, semi-automated or completely automated. The BACTEC system (from Becton Dickinson) and the BacTAlert system (from Organon Teknika Corporation) are the two most widely used automated blood culture systems. These systems incubate blood culture bottles under optimal conditions for bacterial growth. Bacterial growth is monitored continuously to detect early positives by using highly sensitive bacterial growth detectors. Once growth is detected, a Gram stain is performed directly from the blood culture and then used to inoculate nutrient agar plates. Subsequently, bacterial identification and susceptibility testing are carried out from isolated bacterial colonies with automated systems as described previously. The bottles are normally reported as negative if no growth is detected after an incubation of 6 to 7 days. Normally, the vast majority of blood cultures are reported negative. For example, the percentage of negative blood cultures at the microbiology laboratory of the CHUL for the period February 1994-January 1995 was 93.1% (Table 3).

[0012] Other Clinical Samples

[0013] Upon receipt by the clinical microbiology laboratory, all body fluids other than blood and urine that are from normally sterile sites (i.e. cerebrospinal, synovial, pleural, pericardial and others) are processed for direct microscopic examination and subsequent culture. Again, most clinical samples are negative for culture (Table 3).

[0014] Regarding clinical specimens which are not from sterile sites such as sputum or stool specimens, the laboratory diagnosis by culture is more problematic because of the contamination by the normal flora. The bacterial pathogens potentially associated with the infection are purified from the contaminants and then identified as described previously. Of course, the universal detection of bacteria would not be useful for the diagnosis of bacterial infections at these non sterile sites. On the other hand, DNA-based assays for species or genus detection and identification as well as for the detection of antibiotic resistance genes from these specimens would be very useful and would offer several advantages over classical identification and susceptibility testing methods.

[0015] DNA-Based Assays with any Clinical Specimens

[0016] There is an obvious need for rapid and accurate diagnostic tests for bacterial detection and identification directly from clinical specimens. DNA-based technologies are rapid and accurate and offer a great potential to improve the diagnosis of infectious diseases (Persing et al., 1993, Diagnostic Molecular Microbiology: Principles and Applications, American Society for Microbiology, Washington, D.C.). The DNA probes and amplification primers which are objects of the present invention are applicable for bacterial or fungal detection and identification directly from any clinical specimens such as blood cultures, blood, urine, sputum, cerebrospinal fluid, pus and other type of specimens (Table 3). The DNA-based tests proposed in this invention are superior in terms of both rapidity and accuracy to standard biochemical methods currently used for routine diagnosis from any clinical specimens in microbiology laboratories. Since these tests are performed in around only one hour, they provide the clinicians with new diagnostic tools which should contribute to increase the efficiency of therapies with antimicrobial agents. Clinical specimens from organisms other than humans (e.g. other primates, birds, plants, mammals, farm animals, livestock and others) may also be tested with these assays.

[0017] A High Percentage of Culture Negative Specimens

[0018] Among all the clinical specimens received for routine diagnosis, approximately 80% of urine specimens and even more (around 95%) for other types of clinical specimens are negative for the presence of bacterial pathogens (Table 3). It would also be desirable, in addition to identify bacteria at the species or genus level in a given specimen, to screen out the high proportion of negative clinical specimens with a test detecting the presence of any bacterium (i.e. universal bacterial detection). Such a screening test may be based on the DNA amplification by PCR of a highly conserved genetic target found in all bacteria. Specimens negative for bacteria would not be amplified by this assay. On the other hand, those that are positive for bacteria would give a positive amplification signal with this assay.

[0019] Towards the Development of Rapid DNA-Based Diagnostic Tests

[0020] A rapid diagnostic test should have a significant impact on the management of infections. DNA probe and DNA amplification technologies offer several advantages over conventional methods for the identification of pathogens and antibiotic resistance genes from clinical samples (Persing et al., 1993, Diagnostic Molecular Microbiology: Principles and Applications, American Society for Microbiology, Washington, D.C.; Ehrlich and Greenberg, 1994, PCR-based Diagnostics in Infectious Disease, Blackwell Scientific Publications, Boston, Mass.). There is no need for culture of the bacterial pathogens, hence the organisms can be detected directly from clinical samples, thereby reducing the time associated with the isolation and identification of pathogens. Furthermore, DNA-based assays are more accurate for bacterial identification than currently used phenotypic identification systems which are based on biochemical tests. Commercially available DNA-based technologies are currently used in clinical microbiology laboratories, mainly for the detection and identification of fastidious bacterial pathogens such as Mycobacterium tuberculosis, Chlamydia trachomatis, Neisseria gonorrhoeae as well as for the detection of a variety of viruses (Podzorski and Persing, Molecular detection and identification of microorganisms, In: P. Murray et al., 1995, Manual of Clinical Microbiology, ASM press, Washington D.C.). There are also other commercially available DNA-based assays which are used for culture confirmation assays.

[0021] Others have developed DNA-based tests for the detection and identification of bacterial pathogens which are objects of the present invention: Staphylococcus spp. (U.S. Pat. No. 5,437,978), Neisseria spp. (U.S. Pat. No. 5,162,199 and European patent publication No. EP 0 337 896 131) and Listeria monocytogenes (U.S. Pat. Nos. 5,389,513 and 5,089,386). However, the diagnostic tests described in these patents are based either on rRNA genes or on genetic targets different from those described in the present invention.

[0022] Although there are diagnostic kits or methods already used in clinical microbiology laboratories, there is still a need for an advantageous alternative to the conventional culture identification methods in order to improve the accuracy and the speed of the diagnosis of commonly encountered bacterial infections. Besides being much faster, DNA-based diagnostic tests are more accurate than standard biochemical tests presently used for diagnosis because the bacterial genotype (e.g. DNA level) is more stable than the bacterial phenotype (e.g. metabolic level).

[0023] Knowledge of the genomic sequences of bacterial and fungal species continuously increases as testified by the number of sequences available from databases. From the sequences readily available from databases, there is no indication therefrom as to their potential for diagnostic purposes. For determining good candidates for diagnostic purposes, one could select sequences for DNA-based assays for (i) the species-specific detection and identification of commonly encountered bacterial or fungal pathogens, (ii) the genus-specific detection and identification of commonly encountered bacterial or fungal pathogens, (iii) the universal detection of bacterial or fungal pathogens and/or (iv) the specific detection and identification of antibiotic resistance genes. All of the above types of DNA-based assays may be performed directly from any type of clinical specimens or from a microbial culture.

[0024] In WO 96/08502 patent publication, we described DNA sequences suitable for (i) the species-specific detection and identification of 12 clinically important bacterial pathogens, (ii) the universal detection of bacteria, and (iii) the detection of 17 antibiotic resistance genes. This co-pending application described proprietary DNA sequences and DNA sequences selected from databases (in both cases, fragments of at least 100 base pairs), as well as oligonucleotide probes and amplification primers derived from these sequences. All the nucleic acid sequences described in this patent application enter the composition of diagnostic kits and methods capable of a) detecting the presence of bacteria, b) detecting specifically the presence of 12 bacterial species and 17 antibiotic resistance genes. However, these methods and kits need to be improved, since the ideal kit and method should be capable of diagnosing close to 100% of microbial pathogens and antibiotic resistance genes. For example, infections caused by Enterococcus faecium have become a clinical problem because of its resistance to many antibiotics. Both the detection of these bacteria and the evaluation of their resistance profiles are desirable. It is worthwhile noting that the French patent publication FR-A-2,699,539 discloses the sequence of vancomycin B gene, which gene may be derived from Enterococcus faecium strains resistant to this antibiotic. Besides that, novel DNA sequences (probes and primers) capable of recognizing the same and other microbial pathogens or the same and additional antibiotic resistance genes are also desirable to aim at detecting more target genes and complement our earlier patent application.

STATEMENT OF THE INVENTION

[0025] It is an object of the present invention to provide a specific, ubiquitous and sensitive method using probes and/or amplification primers for determining the presence and/or amount of nucleic acids:

[0026] from specific microbial species or genera selected from the group consisting of Streptococcus species, Streptococcus agalactiae, Staphylococcus species, Staphylococcus saprophyticus, Enterococcus species, Enterococcus faecium, Neisseria species, Neisseria meningitidis, Listeria monocytogenes, Candida species and Candida albicans

[0027] from an antibiotic resistance gene selected from the group consisting of bla_(tem), bla_(rob), bla_(shv), bla_(oxa), blaZ, aadB, aacC1, aacC2, aacC3, aacA4, aac6′-lla, ermA, ermB, ermC, mecA, vanA, vanB, vanC, satA, aac(6′)-aph(2″), aad(6′), vat, vga, msrA, sul and int, and optionally,

[0028] from any bacterial species

[0029] in any sample suspected of containing said nucleic acids,

[0030] wherein each of said nucleic acids or a variant or part thereof comprises a selected target region hybridizable with said probe or primers;

[0031] said method comprising the steps of contacting said sample with said probes or primers and detecting the presence and/or amount of hybridized probes or amplified products as an indication of the presence and/or amount of said any bacterial species, specific microbial species or genus and antibiotic resistance gene.

[0032] In a specific embodiment, a similar method directed to each specific microbial species or genus detection and identification, antibiotic resistance genes detection, and universal bacterial detection, separately, is provided.

[0033] In a more specific embodiment, the method makes use of DNA fragments (proprietary fragments and fragments obtained from databases), selected for their capacity to sensitively, specifically and ubiquitously detect the targeted bacterial or fungal nucleic acids.

[0034] In a particularly preferred embodiment, oligonucleotides of at least 12 nucleotides in length have been derived from the longer DNA fragments, and are used in the present method as probes or amplification primers.

[0035] The proprietary oligonucleotides (probes and primers) are also another object of the invention.

[0036] Diagnostic kits comprising probes or amplification primers for the detection of a microbial species or genus selected from the group consisting of Streptococcus species, Streptococcus agalactiae, Staphylococcus species, Staphylococcus saprophyticus, Enterococcus species, Enterococcus faecium, Neisseria species, Neisseria meningitidis, Listeria monocytogenes, Candida species and Candida albicans are also objects of the present invention.

[0037] Diagnostic kits further comprising probes or amplification primers for the detection of an antibiotic resistance gene selected from the group consisting of bla_(tem), bla_(rob), bla_(shv), bla_(oxa), blaZ, aadB, aacC1, aacC2, aacC3, aacA4, aac6′-lla, ermA, ermB, ermC, mecA, vanA, vanB, vanC, satA, aac(6′)-aph(2″), aad(6′), vat, vga, msrA, sul and int are also objects of this invention.

[0038] Diagnostic kits further comprising probes or amplification primers for the detection of any bacterial or fungal species, comprising or not comprising those for the detection of the specific microbial species or genus listed above, and further comprising or not comprising probes and primers for the antibiotic resistance genes listed above, are also objects of this invention.

[0039] In a preferred embodiment, such a kit allows for the separate or the simultaneous detection and identification of the above-listed microbial species or genus, antibiotic resistance genes and for the detection of any bacterium.

[0040] In the above methods and kits, amplification reactions may include a) polymerase chain reaction (PCR), b) ligase chain reaction, c) nucleic acid sequence-based amplification, d) self-sustained sequence replication, e) strand displacement amplification, f) branched DNA signal amplification, g) transcription-mediated amplification, h) cycling probe technology (CPT) i) nested PCR, or j) multiplex PCR.

[0041] In a preferred embodiment, a PCR protocol is used as an amplification reaction.

[0042] In a particularly preferred embodiment, a PCR protocol is provided, comprising, for each amplification cycle, an annealing step of 30 seconds at 45-55° C. and a denaturation step of only one second at 95° C., without any time allowed specifically for the elongation step. This PCR protocol has been standardized to be suitable for PCR reactions with all selected primer pairs, which greatly facilitates the testing because each clinical sample can be tested with universal, species-specific, genus-specific and antibiotic resistance gene PCR primers under uniform cycling conditions. Furthermore, various combinations of primer pairs may be used in multiplex PCR assays.

[0043] We aim at developing a rapid test or kit to discard rapidly all the samples which are negative for bacterial cells and to subsequently detect and identify the above bacterial and/or fungal species and genera and to determine rapidly the bacterial resistance to antibiotics. Although the sequences from the selected antibiotic resistance genes are available from databases and have been used to develop DNA-based tests for their detection, our approach is unique because it represents a major improvement over current gold standard diagnostic methods based on bacterial cultures. Using an amplification method for the simultaneous bacterial detection and identification and antibiotic resistance genes detection, there is no need for culturing the clinical sample prior to testing. Moreover, a modified PCR protocol has been developed to detect all target DNA sequences in approximately one hour under uniform amplification conditions. This procedure will save lives by optimizing treatment, will diminish antibiotic resistance because less antibiotics will be prescribed, will reduce the use of broad spectrum antibiotics which are expensive, decrease overall health care costs by preventing or shortening hospitalizations, and decrease the time and costs associated with clinical laboratory testing.

[0044] In the methods and kits described herein below, the oligonucleotide probes and amplification primers have been derived from larger sequences (i.e. DNA fragments of at least 100 base pairs). All DNA fragments have been obtained either from proprietary fragments or from databases. DNA fragments selected from databases are newly used in a method of detection according to the present invention, since they have been selected for their diagnostic potential.

[0045] It is clear to the individual skilled in the art that other oligonucleotide sequences appropriate for (i) the universal bacterial detection, (ii) the detection and identification of the above microbial species or genus and (iii) the detection of antibiotic resistance genes other than those listed in Annex VI may also be derived from the proprietary fragments or selected database sequences. For example, the oligonucleotide primers or probes may be shorter or longer than the ones we have chosen; they may also be selected anywhere else in the proprietary DNA fragments or in the sequences selected from databases; they may be also variants of the same oligonucleotide. If the target DNA or a variant thereof hybridizes to a given oligonucleotide, or if the target DNA or a variant thereof can be amplified by a given oligonucleotide PCR primer pair, the converse is also true; a given target DNA may hybridize to a variant oligonucleotide probe or be amplified by a variant oligonucleotide PCR primer. Alternatively, the oligonucleotides may be designed from any DNA fragment sequences for use in amplification methods other than PCR. Consequently, the core of this invention is the identification of universal, species-specific, genus-specific and resistance gene-specific genomic or non-genomic DNA fragments which are used as a source of specific and ubiquitous oligonucleotide probes and/or amplification primers. Although the selection and evaluation of oligonucleotides suitable for diagnostic purposes requires much effort, it is quite possible for the individual skilled in the art to derive, from the selected DNA fragments, oligonucleotides other than the ones listed in Annex VI which are suitable for diagnostic purposes. When a proprietary fragment or a database sequence is selected for its specificity and ubiquity, it increases the probability that subsets thereof will also be specific and ubiquitous.

[0046] Since a high percentage of clinical specimens are negative for bacteria (Table 3), DNA fragments having a high potential for the selection of universal oligonucleotide probes or primers were selected from proprietary and database sequences. The amplification primers were selected from a gene highly conserved in bacteria and fungi, and are used to detect the presence of any bacterial pathogen in clinical specimens in order to determine rapidly (approximately one hour) whether it is positive or negative for bacteria. The selected gene, designated tuf, encodes a protein (EF-Tu) involved in the translational process during protein synthesis. The tuf gene sequence alignments used to derive the universal primers include both proprietary and database sequences (Example 1 and Annex I). This strategy allows the rapid screening of the numerous negative clinical specimens (around 80% of the specimens received, see Table 3) submitted for bacteriological testing. Tables 4, 5 and 6 provide a list of the bacterial or fungal species used to test the specificity of PCR primers and DNA probes. Table 7 gives a brief description of each species-specific, genus-specific and universal amplification assays which are objects of the present invention. Tables 8, 9 and 10 provide some relevant information about the proprietary and database sequences selected for diagnostic puposes.

DETAILED DESCRIPTION OF THE INVENTION

[0047] Development of Species-Specific, Genus-Specific, Universal and Antibiotic Resistance Gene-Specific DNA Probes and Amplification Primers for Microorganisms

[0048] Selection from Databases of Sequences Suitable for Diagnostic Purposes

[0049] In order to select sequences which are suitable for species-specific or genus-specific detection and identification of bacteria or fungi or, alternatively, for the universal detection of bacteria, the database sequences (GenBank, EMBL and Swiss-Prot) were chosen based on their potential for diagnostic purposes according to sequence information and computer analysis performed with these sequences. Initially, all sequence data available for the targeted microbial species or genus were carefully analyzed. The gene sequences which appeared the most promising for diagnostic purposes based on sequence information and on sequence comparisons with the corresponding gene in other microbial species or genera performed with the Genetics Computer Group (GCG, Wisconsin) programs were selected for testing by PCR. Optimal PCR amplification primers were chosen from the selected database sequences with the help of the Oligo™ 4.0 primer analysis software (National Biosciences Inc., Plymouth, Minn.). The chosen primers were tested in PCR assays for their specificity and ubiquity for the target microbial species or genus. In general, the identification of database sequences from which amplification primers suitable for species-specific or genus-specific detection and identification were selected involved the computer analysis and PCR testing of several candidate gene sequences before obtaining a primer pair which is specific and ubiquitous for the target microbial species or genus. Annex VI provides a list of selected specific and ubiquitous PCR primer pairs. Annexes I to V and Examples 1 to 4 illustrate the strategy used to select genus-specific, species-specific and universal PCR primers from tuf sequences or from the recA gene.

[0050] Oligonucleotide Primers and Probes Design and Synthesis

[0051] The DNA fragments sequenced by us or selected from databases (GenBank and EMBL) were used as sources of oligonucleotides for diagnostic purposes. For this strategy, an array of suitable oligonucleotide primers or probes derived from a variety of genomic DNA fragments (size of more than 100 bp) selected from databases were tested for their specificity and ubiquity in PCR and hybridization assays as described later. It is important to note that the database sequences were selected based on their potential for being species-specific, genus-specific or universal for the detection of bacteria or fungi according to available sequence information and extensive analysis and that, in general, several candidate database sequences had to be tested in order to obtain the desired specificity, ubiquity and sensitivity.

[0052] Oligonucleotide probes and amplification primers derived from species-specific fragments selected from database sequences were synthesized using an automated DNA synthesizer (Perkin-Elmer Corp., Applied Biosystems Division). Prior to synthesis, all oligonucleotides (probes for hybridization and primers for DNA amplification) were evaluated for their suitability for hybridization or DNA amplification by polymerase chain reaction (PCR) by computer analysis using standard programs (i.e. the Genetics Computer Group (GCG) programs and the primer analysis software Oligo™ 4.0). The potential suitability of the PCR primer pairs was also evaluated prior to the synthesis by verifying the absence of unwanted features such as long stretches of one nucleotide and a high proportion of G or C residues at the 3′ end (Persing et al., 1993, Diagnostic Molecular Microbiology: Principles and Applications, American Society for Microbiology, Washington, D.C.).

[0053] The oligonucleotide primers or probes may be derived from either strand of the duplex DNA. The primers or probes may consist of the bases A, G, C, or T or analogs and they may be degenerated at one or more chosen nucleotide position(s). The primers or probes may be of any suitable length and may be selected anywhere within the DNA sequences from proprietary fragments or from selected database sequences which are suitable for (i) the universal detection of bacteria, (ii) the species-specific detection and identification of Enterococcus faecium, Listeria monocytogenes, Neisseria meningitidis, Staphylococcus saprophyticus, Streptococcus agalactiae and Candida albicans (iii) the genus-specific detection of Streptococcus species, Enterococcus species, Staphylococcus species and Neisseria species or (iv) the detection of the 26 above-mentioned clinically important antibiotic resistance genes.

[0054] Variants for a given target bacterial gene are naturally occurring and are attributable to sequence variation within that gene during evolution (Watson et al., 1987, Molecular Biology of the Gene, 4^(th) ed., The Benjamin/Cummings Publishing Company, Menlo Park, Calif.; Lewin, 1989, Genes IV, John Wiley & Sons, New York, N.Y.). For example, different strains of the same bacterial species may have a single or more nucleotide variation(s) at the oligonucleotide hybridization site. The person skilled in the art is well aware of the existence of variant bacterial or fungal DNA sequences for a specific gene and that the frequency of sequence variations depends on the selective pressure during evolution on a given gene product. The detection of a variant sequence for a region between two PCR primers may be demonstrated by sequencing the amplification product. In order to show the presence of sequence variants at the primer hybridization site, one has to amplify a larger DNA target with PCR primers outside that hybridization site. Sequencing of this larger fragment will allow the detection of sequence variation at this site. A similar strategy may be applied to show variants at the hybridization site of a probe. Insofar as the divergence of the target sequences or a part thereof does not affect the specificity and ubiquity of the amplification primers or probes, variant bacterial DNA is under the scope of this invention. Variants of the selected primers or probes may also be used to amplify or hybridize to a variant DNA.

[0055] Sequencing of Tuf Sequences from a variety of Bacterial and Fungal Species

[0056] The nucleotide sequence of a portion of tuf genes was determined for a variety of bacterial and fungal species. The amplification primers SEQ ID NOs: 107 and 108, which amplify a tuf gene portion of approximately 890 bp, were used for the sequencing of bacterial tuf sequences. The amplification primers SEQ ID NOs: 109 and 172, which amplify a tuf gene portion of approximately 830 bp, were used for the sequencing of fungal tuf sequences. Both primer pairs can amplify tufA and tufB genes. This is not surprising because these two genes are nearly identical. For example, the entire tufA and tufB genes from E. coli differ at only 13 nucleotide positions (Neidhardt et al., 1996, Escherichia coil and Salmonella: Cellular and Molecular Biology, 2^(nd) ed., American Society for Microbiology Press, Washington, D.C.). These amplification primers are degenerated at several nucleotide positions and contain inosines in order to allow the amplification of a wide range of tuf sequences. The strategy used to select these amplification primers is similar to that illustrated in Annex I for the selection of universal primers. The amplification primers SEQ ID NOs: 107 and 108 could be used to amplify the tuf genes from any bacterial species. The amplification primers SEQ ID NOs: 109 and 172 could be used to amplify the tuf genes from any fungal species.

[0057] The tuf genes were amplified directly from bacterial or yeast cultures using the following amplification protocol: One μL of cell suspension was transferred directly to 19 μL of a PCR reaction mixture containing 50 mM KCl, 10 mM Tris-HCl (pH 9.0), 0.1% Triton X-100, 2.5 mM MgCl₂, 1 μM of each of the 2 primers, 200 μM of each of the four dNTPs, 0.5 unit of Taq DNA polymerase (Promega Corp., Madison, Wis.). PCR reactions were subjected to cycling using a MJ Research PTC-200 thermal cycler (MJ Research Inc., Watertown, Mass.) as follows: 3 min at 96° C. followed by 30-35 cycles of 1 min at 95° C. for the denaturation step, 1 min at 30-50° C. for the annealing step and 1 min at 72° C. for the extension step. Subsequently, twenty microliters of the PCR-amplified mixture were resolved by electrophoresis in a 1.5% agarose gel. The gel was then visualized by staining with methylene blue (Flores et al., 1992, Biotechniques, 13:203-205). The size of the amplification products was estimated by comparison with a 100-bp molecular weight ladder. The band corresponding to the specific amplification product (i.e. approximately 890 or 830 bp for bacterial or fungal tuf sequences, respectively) was excised from the agarose gel and purified using the QIAquick™ gel extraction kit (QIAGEN Inc., Chatsworth, Calif.). The gel-purified DNA fragment was then used directly in the sequencing protocol. Both strands of the tuf genes amplification product were sequenced by the dideoxynucleotide chain termination sequencing method by using an Applied Biosystems automated DNA sequencer (model 373A) with their PRISM™ Sequenase® Terminator Double-stranded DNA Sequencing Kit (Perkin-Elmer Corp., Applied Biosystems Division, Foster City, Calif.). The sequencing reactions were all performed by using the amplification primers (SEQ ID NOs: 107 to 109 and 172) and 100 ng per reaction of the gel-purified amplicon. In order to ensure that the determined sequence did not contain errors attributable to the sequencing of PCR artefacts, we have sequenced two preparations of the gel-purified tuf amplification product originating from two independent PCR amplifications. For all target microbial species, the sequences determined for both amplicon preparations were identical. Furthermore, the sequences of both strands were 100% complementary thereby confirming the high accuracy of the determined sequence. The tuf sequences determined using the above strategy are all in the Sequence Listing (i.e. SEQ ID NOs:118 to 146). Table 13 gives the originating microbial species and the source for each tuf sequence in the Sequence Listing.

[0058] The alignment of the tuf sequences determined by us or selected from databases reveals clearly that the length of the sequenced portion of the tuf genes is variable. There may be insertions or deletions of several amino acids. This explains why the size of the sequenced tuf amplification product was variable for both bacterial and fungal species. Among the tuf sequences determined by our group, we found insertions and deletions adding up to 5 amino acids or 15 nucleotides. Consequently, the nucleotide positions indicated on top of each of Annexes I to V do not correspond for tuf sequences having insertions or deletions.

[0059] It should also be noted that the various tuf sequences determined by us occasionally contain degenerescences. These degenerated nucleotides correspond to sequence variations between tufA and tufB genes because the amplification primers amplify both tuf genes. These nucleotide variations were not attributable to nucleotide misincorporations by the taq DNA polymerase because the sequence of both strands were identical and also because the sequences determined with both preparations of the gel-purified tuf amplicons were identical.

[0060] The Selection of Amplification Primers from Tuf Sequences

[0061] The tuf sequences determined by us or selected from databases were used to select PCR primers for (i) the universal detection of bacteria, (ii) the genus-specific detection and identification of Enterococcus spp. and Staphylococcus spp. and (iii) the species-specific detection and identification of Candida albicans. The strategy used to select these PCR primers was based on the analysis of multiple sequence alignments of various tuf sequences. For more details about the selection of PCR primers from tuf sequences, please refer to Examples 1 to 3 and Annexes I to IV.

[0062] The Selection of Amplification Primers from recA

[0063] The comparison of the nucleotide sequence for the recA gene from various bacterial species including 5 species of streptococci allowed the selection of Streptococcus-specific PCR primers. For more details about the selection of PCR primers from recA, please refer to Example 4 and Annex V.

[0064] DNA Fragment Isolation from Staphylococcus saprophyticus by Arbitrarily Primed PCR

[0065] DNA sequences of unknown coding potential for the species-specific detection and identification of Staphylococcus saprophyticus were obtained by the method of arbitrarily primed PCR (AP-PCR).

[0066] AP-PCR is a method which can be used to generate specific DNA probes for microorganisms (Fani et al., 1993, Mol. Ecol. 2:243-250). A description of the AP-PCR protocol used to isolate a species-specific genomic DNA fragment from Staphylococcus saprophyticus follows. Twenty different oligonucleotide primers of 10 nucleotides in length (all included in the AP-PCR kit OPAD (Operon Technologies, Inc., Alameda, Calif.)) were tested systematically with DNAs from 3 bacterial strains of Staphylococcus saprophyticus (all obtained from the American Type Culture Collection (ATCC): numbers 15305, 35552 and 43867) as well as with DNA from four other staphylococcal species (Staphylococcus aureus ATCC 25923, Staphylococcus epidermidis ATCC 14990, Staphylococcus haemolyticus ATCC 29970 and Staphylococcus hominis ATCC 35982). For all bacterial species, amplification was performed from a bacterial suspension adjusted to a standard 0.5 McFarland which corresponds to approximately 1.5×10⁸ bacteria/mL. One μL of the standardized bacterial suspension was transferred directly to 19 μL of a PCR reaction mixture containing 50 mM KCl, 10 mM Tris-HCI (pH 9.0), 0.1% Triton X-100, 2.5 mM MgCl₂, 1.2 μM of only one of the 20 different AP-PCR primers OPAD, 200 μM of each of the four dNTPs and 0.5 unit of Taq DNA polymerase (Promega Corp., Madison, Wis.). PCR reactions were subjected to cycling using a MJ Research PTC-200 thermal cycler (MJ Research Inc.) as follows: 3 min at 96° C. followed by 35 cycles of 1 min at 95° C. for the denaturation step, 1 min at 32° C. for the annealing step and 1 min at 72° C. for the extension step. A final extension step of 7 min at 72° C. was made after the 35 cycles to ensure complete extension of PCR products. Subsequently, twenty microliters of the PCR amplified mixture were resolved by electrophoresis in a 2% agarose gel containing 0.25 μg/mL of ethidium bromide. The size of the amplification products was estimated by comparison with a 50-bp molecular weight ladder.

[0067] Amplification patterns specific for Staphylococcus saprophyticus were observed with the AP-PCR primer OPAD-9 (SEQ ID NO: 25). Amplification with this primer consistently showed a band corresponding to a DNA fragment of approximately 450 bp for all Staphylococcus saprophyticus strains tested but not for any of the four other staphylococcal species tested. This species-specific pattern was confirmed by testing 10 more clinical isolates of S. saprophyticus selected from the culture collection of the microbiology laboratory of the CHUL as well as strains selected from the gram-positive bacterial species listed in Table 5.

[0068] The band corresponding to the approximately 450 bp amplicon which was specific and ubiquitous for S. saprophyticus based on AP-PCR was excised from the agarose gel and purified using the QIAquick™ gel extraction kit (QIAGEN Inc.). The gel-purified DNA fragment was cloned into the T/A cloning site of the pCR 2.1™ plasmid vector (Invitrogen Inc.) using T4 DNA ligase (New England BioLabs). Recombinant plasmids were transformed into E. coli DH5α competent cells using standard procedures. Plasmid DNA isolation was done by the method of Birnboirn and Doly (Nucleic Acids Res. 7:1513-1523) for small-scale preparations. All plasmid DNA preparations were digested with the EcoRI restriction endonuclease to ensure the presence of the approximately 450 bp AP-PCR insert into the recombinant plasmids. Subsequently, a large-scale and highly purified plasmid DNA preparation was performed from two selected clones shown to carry the AP-PCR insert by using the QIAGEN plasmid purification kit. These plasmid preparations were used for automated DNA sequencing.

[0069] Both strands of the AP-PCR insert from the two selected clones were sequenced by the dideoxynucleotide chain termination sequencing method with SP6 and T7 sequencing primers, by using an Applied Biosystems automated DNA sequencer as described previously. The analysis of the obtained sequences revealed that the DNA sequences for both strands from each clone were 100% complementary. Furthermore, it showed that the entire sequence determined for each clone were both identical. These sequencing data confirm the 100% accuracy for the determined 438 bp sequence (SEQ ID NO: 29). Optimal amplification primers have been selected from the sequenced AP-PCR Staphylococcus saprophyticus DNA fragment with the help of the primer analysis software Oligotm 4.0. The selected primer sequences have been tested in PCR assays to verify their specificity and ubiquity (Table 7). These PCR primers were specific since there was no amplification with DNA from bacterial species other than S. saprophyticus selected from Tables 4 and 5. Furthermore, this assay was ubiquitous since 245 of 260 strains of S. saprophyticus were efficiently amplified with this PCR assay. When used in combination with another S. saprophyticus-specific PCR assay, which is an object of our co-pending U.S. (Ser. No. 08/526,840) and PCT (PCT/CA/95/00528) patent applications, the ubiquity reaches 100% for these 260 strains.

[0070] DNA Amplification

[0071] For DNA amplification by the widely used PCR (polymerase chain reaction) method, primer pairs were derived from proprietary DNA fragments or from database sequences. Prior to synthesis, the potential primer pairs were analyzed by using the Oligo™ 4.0 software to verify that they are good candidates for PCR amplification.

[0072] During DNA amplification by PCR, two oligonucleotide primers binding respectively to each strand of the heat-denatured target DNA from the bacterial genome are used to amplify exponentially in vitro the target DNA by successive thermal cycles allowing denaturation of the DNA, annealing of the primers and synthesis of new targets at each cycle (Persing et al, 1993, Diagnostic Molecular Microbiology: Principles and Applications, American Society for Microbiology, Washington, D.C.).

[0073] Briefly, the PCR protocols were as follow: Treated clinical specimens or standardized bacterial or fungal suspensions (see below) were amplified in a 20 μL PCR reaction mixture containing 50 mM KCl, 10 mM Tris-HCl (pH 9.0), 2.5 mM MgCl₂, 0.4 μM of each primer, 200 μM of each of the four dNTPs and 0.5 unit of Taq DNA polymerase (Promega) combined with the TaqStart™ antibody (Clontech Laboratories Inc., Palo Alto, Calif.). The TaqStart™ antibody, which is a neutralizing monoclonal antibody to Taq DNA polymerase, was added to all PCR reactions to enhance the specificity and the sensitivity of the amplifications (Kellogg et al., 1994, Biotechniques 16:1134-1137). The treatment of the clinical specimens varies with the type of specimen tested, since the composition and the sensitivity level required are different for each specimen type. It consists in a rapid protocol to lyse the bacterial cells and eliminate the PCR inhibitory effects (see example 11 for urine specimen preparation). For amplification from bacterial or fungal cultures, the samples were added directly to the PCR amplification mixture without any pretreatment step (see example 10). Primer sequences derived from highly conserved regions of the bacterial 16S ribosomal RNA gene were used to provide an internal control for all PCR reactions. Alternatively, the internal control was derived from sequences not found in microorganisms or in the human genome. The internal control was integrated into all amplification reactions to verify the efficiency of the PCR assays and to ensure that significant PCR inhibition was absent. The internal control derived from rRNA was also useful to monitor the efficiency of bacterial lysis protocols.

[0074] PCR reactions were then subjected to thermal cycling (3 min at 95° C. followed by 30 cycles of 1 second at 95° C. for the denaturation step and 30 second at 55° C. for the annealing-extension step) using a PTC-200 thermal cycler (MJ Research Inc.) and subsequently analyzed by standard ethidium bromide-stained agarose gel electrophoresis. The number of cycles performed for the PCR assays varies according to the sensitivity level required. For example, the sensitivity level required for microbial detection directly from clinical specimens is higher for blood specimens than for urine specimens because the concentration of microorganisms associated with a septicemia can be much lower than that associated with a urinary tract infection. Consequently, more sensitive PCR assays having more thermal cycles are required for direct detection from blood specimens. Similarly, PCR assays performed directly from bacterial or fungal cultures may be less sensitive than PCR assays performed directly from clinical specimens because the number of target organisms is normally much lower in clinical specimens than in microbial cultures.

[0075] It is clear that other methods for the detection of specific amplification products, which may be faster and more practical for routine diagnosis, may be used. Such methods may be based on the detection of fluorescence after amplification (e.g. TaqMan™ system from Perkin Elmer or Amplisensor™ from Biotronics). Methods based on the detection of fluorescence are particularly promising for utilization in routine diagnosis as they are very rapid, quantitative and can be automated (Example 14).

[0076] Microbial pathogens detection and identification may also be performed by solid support or liquid hybridization using species-specific internal DNA probes hybridizing to an amplification product. Such probes may be generated from any species-specific or genus-specific DNA amplification products which are objects of the present invention. Alternatively, the internal probes for species or genus detection and identification may be derived from the amplicons produced by the universal amplification assay. The oligonucleotide probes may be labeled with biotin or with digoxigenin or with any other reporter molecules.

[0077] To assure PCR efficiency, glycerol, dimethyl sulfoxide (DMSO) or other related solvents can be used to increase the sensitivity of the PCR and to overcome problems associated with the amplification of a target DNA having a high GC content or forming strong secondary structures (Dieffenbach and Dveksler, 1995, PCR Primer : A Laboratory Manual, Cold Spring Harbor Laboratory Press, Plainview, N.Y.). The concentration ranges for glycerol and DMSO are 5-15% (v/v) and 3-10% (v/v), respectively. For the PCR reaction mixture, the concentration ranges for the amplification primers and MgCl₂ are 0.1-1.5 μM and 1.5-3.5 mM, respectively. Modifications of the standard PCR protocol using external and nested primers (i.e. nested PCR) or using more than one primer pair (i.e. multiplex PCR) may also be used (Persing et al., 1993, Diagnostic Molecular Microbiology: Principles and Applications, American Society for Microbiology, Washington, D.C.). For more details about the PCR protocols and amplicon detection methods, see Examples 9 to 14.

[0078] The person skilled in the art of DNA amplification knows the existence of other rapid amplification procedures such as ligase chain reaction (LCR), transcription-mediated amplification (TMA), self-sustained sequence replication (3SR), nucleic acid sequence-based amplification (NASBA), strand displacement amplification (SDA), branched DNA (bDNA) and cycling probe technology (CPT) (Lee et al., 1997, Nucleic Acid Amplification Technologies: Application to Disease Diagnosis, Eaton Publishing, Boston, Mass.; Persing et al., 1993, Diagnostic Molecular Microbiology: Principles and Applications, American Society for Microbiology, Washington, D.C.). The scope of this invention is not limited to the use of amplification by PCR, but rather includes the use of any rapid nucleic acid amplification method or any other procedure which may be used to increase rapidity and sensitivity of the tests. Any oligonucleotide suitable for the amplification of nucleic acids by approaches other than PCR and derived from the species-specific, genus-specific and universal DNA fragments as well as from selected antibiotic resistance gene sequences included in this document are also under the scope of this invention.

[0079] Hybridization Assays with Oligonucleotide Probes

[0080] In hybridization experiments, single-stranded oligonucleotides (size less than 100 nucleotides) have some advantages over DNA fragment probes for the detection of bacteria, such as ease of synthesis in large quantities, consistency in results from batch to batch and chemical stability. Briefly, for the hybridizations, oligonucleotides were 5′ end-labeled with the radionucleotide y-³²P(dATP) using T4 polynucleotide kinase (Pharmacia) (Sambrook et al., 1989, Molecular Cloning: A Laboratory Manual, 2^(nd) ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.). The unincorporated radionucleotide was removed by passing the labeled oligonucleotide through a Sephadex G-50™ column. Alternatively, oligonucleotides were labeled with biotin, either enzymatically at their 3′ ends or incorporated directly during synthesis at their 5′ ends, or with digoxigenin. It will be appreciated by the person skilled in the art that labeling means other than the three above labels may be used.

[0081] Each oligonucleotide probe was then tested for its specificity by hybridization to DNAs from a variety of bacterial and fungal species selected from Tables 4, 5 and 6. All of the bacterial or fungal species tested were likely to be pathogens associated with common infections or potential contaminants which can be isolated from clinical specimens. Each target DNA was released from bacterial cells using standard chemical treatments to lyse the cells (Sambrook et al., 1989, Molecular Cloning: A Laboratory Manual, 2^(nd) ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.). Subsequently, the DNA was denatured by conventional methods and then irreversibly fixed onto a solid support (e.g. nylon or nitrocellulose membranes) or free in solution. The fixed single-stranded target DNAs were then hybridized with the oligonucleotide probe cells (Sambrook et al., 1989, Molecular Cloning: A Laboratory Manual, 2^(nd) ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.). Pre-hybridization conditions were in 1 M NaCl+10% dextran sulfate+1% SDS+100 μg/mL salmon sperm DNA at 65° C. for 15 min. Hybridization was performed in fresh pre-hybridization solution containing the labeled probe at 65° C. overnight. Post-hybridization washing conditions were as follows: twice in 3× SSC containing 1% SDS, twice in 2× SSC containing 1% SDS and twice in 1× SSC containing 1% SDS (all of these washes were at 65° C. for 15 min), and a final wash in 0.1× SSC containing 1% SDS at 25° C. for 15 min. Autoradiography of washed filters allowed the detection of selectively hybridized probes. Hybridization of the probe to a specific target DNA indicated a high degree of similarity between the nucleotide sequence of these two DNAs because of the high stringency of the washes.

[0082] An oligonucleotide probe was considered specific only when it hybridized solely to DNA from the species or genus from which it was isolated. Oligonucleotide probes found to be specific were subsequently tested for their ubiquity (i.e. ubiquitous probes recognized most or all isolates of the target species or genus) by hybridization to microbial DNAs from clinical isolates of the species or genus of interest including ATCC strains. The DNAs from strains of the target species or genus were denatured, fixed onto nylon membranes and hybridized as described above. Probes were considered ubiquitous when they hybridized specifically with the DNA from at least 80% of the isolates of the target species or genus.

[0083] Specificity and Ubiquity Tests for Oligonucleotide Primers and Probes

[0084] The specificity of oligonucleotide primers and probes, derived either from the DNA fragments sequenced by us or selected from databases, was tested by amplification of DNA or by hybridization with bacterial or fungal species selected from those listed in Tables 4, 5 and 6, as described in the two previous sections. Oligonucleotides found to be specific were subsequently tested for their ubiquity by amplification (for primers) or by hybridization (for probes) with bacterial DNAs from isolates of the target species or genus. Results for specificity and ubiquity tests with the oligonucleotide primers are summarized in Table 7. The specificity and ubiquity of the PCR assays using the selected amplification primer pairs were tested directly from cultures (see Examples 9 and 10) of bacterial or fungal species.

[0085] The various species-specific and genus-specific PCR assays which are objects of the present invention are all specific. For the PCR assays specific to bacterial species or genus, this means that DNA isolated from a wide variety of bacterial species, other than that from the target species or genus and selected from Tables 4 and 5, could not be amplified. For the PCR assay specific to Candida albicans, it means there was no amplification with genomic DNA from the fungal species listed in Table 6 as well as with a variety of bacterial species selected from Tables 4 and 5.

[0086] The various species-specific and genus-specific PCR assays which are objects of the present invention are also all ubiquitous (Table 7). (i) The species-specific PCR assays for E. faecium, L. monocytogenes, S. saprophyticus, S. agalactiae and C. albicans amplified genomic DNA from all or most strains of the target species tested, which were obtained from various sources and which are representative of the diversity within each target species (Table 7). The species identification of all of these strains was based on classical biochemical methods which are routinely used in clinical microbiology laboratories. (ii) The genus-specific PCR assays specific for Enterococcus spp., Staphylococcus spp., Streptococcus spp. and Neisseria spp. amplified genomic DNA from all or most strains of the target genus tested, which represent all clinically important bacterial species for each target genus. These strains were obtained from various sources and are representative of the diversity within each target genus. Again, the species identification of all of these strains was based on classical biochemical methods which are routinely used in clinical microbiology laboratories. More specifically, the four genus-specific PCR assays amplified the following species: (1) The Enterococcus-specific assay amplified efficiently DNA from all of the 11 enterococcal species tested including E. avium, E. casselifavus, E. dispar, E. durans, E. faecalis, E. faecium, E. flavescens, E. gallinarum, E. hirae, E. mundtii and E. raffinosus. (2) The Neisseria-specific assay amplified efficiently DNA from all of the 12 neisserial species tested including N. canis, N. cinerea, N. elongata, N. flavescens, N. gonorrhoeae, N. lactamica, N. meningitidis, N. mucosa, N. polysaccharea, N. sicca, N. subflava and N. weaveri. (3) The Staphylococcus-specific assay amplified efficiently DNA from 13 of the 14 staphylococcal species tested including S. aureus, S. auricularis, S. capitis, S. cohnii, S. epidermidis, S. haemolyticus, S. hominis, S. lugdunensis, S. saprophyticus, S. schleiferi, S. simulans, S. warneri and S. xylosus. The staphylococcal species which could not be amplified is S. sciuri. (4) Finally, the Streptococcus-specific assay amplified efficiently DNA from all of the 22 streptococcal species tested including S. agalactiae, S. anginosus, S. bovis, S. constellatus, S. crista, S. dysgalactiae, S. equi, S. gordonii, S. intermedius, S. mitis, S. mutans, S. oralis, S. parasanguis, S. pneumoniae, S. pyogenes, S. salivarius, S. sanguis, S. sabrinus, S. suis, S. uberis, S. vestibularis and S. viridans. On the other hand, the Streptococcus-specific assay did not amplify 3 out of 9 strains of S. mutans and 1 out of 23 strains of S. salivarius, thereby showing a slight lack of ubiquity for these two streptococcal species.

[0087] All specific and ubiquitous amplification primers for each target microbial species or genus or antibiotic resistance gene investigated are listed in Annex VI. Divergence in the sequenced DNA fragments can occur, insofar as the divergence of these sequences or a part thereof does not affect the specificity of the probes or amplification primers. Variant bacterial DNA is under the scope of this invention.

[0088] The PCR amplification primers listed in Annex VI were all tested for their specificity and ubiquity using reference strains as well as clinical isolates from various geographical locations. The 351 reference strains used to test the amplification and hybridization assays (Tables 4, 5 and 6) were obtained from (i) the American Type Culture Collection (ATCC): 85%, (ii) the Laboratoire de santé publique du Québec (LSPQ): 10%, (iii) the Centers for Disease Control and Prevention (CDC): 3% , (iv) the National Culture Type Collection (NCTC): 1% and (v) several other reference laboratories throughout the world: 1%. These reference strains are representative of (i) 90 gram-negative bacterial species (169 strains; Table 4), (ii) 97 gram-positive bacterial species (154 strains; Table 5) and (iii) 12 fungal species (28 strains; Table 6).

[0089] Antibiotic Resistance Genes

[0090] Antimicrobial resistance complicates treatment and often leads to therapeutic failures. Furthermore, overuse of antibiotics inevitably leads to the emergence of bacterial resistance. Our goal is to provide clinicians, in approximately one hour, the needed information to prescribe optimal treatments. Besides the rapid identification of negative clinical specimens with DNA-based tests for universal bacterial detection and the identification of the presence of a specific pathogen in the positive specimens with species- and/or genus-specific DNA-based tests, clinicians also need timely information about the ability of the bacterial pathogen to resist antibiotic treatments. We feel that the most efficient strategy to evaluate rapidly bacterial resistance to antimicrobials is to detect directly from the clinical specimens the most common and clinically important antibiotic resistance genes (i.e. DNA-based tests for the detection of antibiotic resistance genes). Since the sequence from the most important and common bacterial antibiotic resistance genes are available from databases, our strategy was to use the sequence from a portion or from the entire resistance gene to design specific oligonucleotide primers or probes which will be used as a basis for the development of rapid DNA-based tests. The sequence from each of the bacterial antibiotic resistance genes selected on the basis of their clinical relevance (i.e. high incidence and importance) is given in the Sequence Listing. Tables 9 and 10 summarize some characteristics of the selected antibiotic resistance genes. Our approach is unique because the antibiotic resistance genes detection and the bacterial detection and identification are performed simultaneously in multiplex assays under uniform PCR amplification conditions (Example 13).

[0091] Annex VI provides a list of all amplification primers selected from 26 clinically important antibiotic resistance genes which were tested in PCR assays. The various PCR assays for antibiotic resistance genes detection and identification were validated by testing several resistant bacterial isolates known to carry the targeted gene and obtained from various countries. The testing of a large number of strains which do not carry the targeted resistance gene was also performed to ensure that all assays were specific. So far, all PCR assays for antibiotic resistance genes are highly specific and have detected all control resistant bacterial strains known to carry the targeted gene. The results of some clinical studies to validate the array of PCR assays for the detection and identification of antibiotic resistance genes and correlate these DNA-based assays with standard antimicrobials susceptibility testing methods are presented in Tables 11 and 12.

[0092] Universal Bacterial Detection

[0093] In the routine microbiology laboratory, a high percentage of clinical specimens sent for bacterial identification are negative by culture (Table 4). Testing clinical samples with universal amplification primers or universal probes to detect the presence of bacteria prior to specific identification and screen out the numerous negative specimens is thus useful as it saves costs and may rapidly orient the clinical management of the patients. Several amplification primers and probes were therefore synthesized from highly conserved portions of bacterial sequences from the tuf genes (Table 8). The universal primer selection was based on a multiple sequence alignment constructed with sequences determined by us or selected from available database sequences as described in Example 1 and Annex I.

[0094] For the identification of database sequences suitable for the universal detection of bacteria, we took advantage of the fact that the complete genome sequences for two distant microorganisms (i.e. Mycoplasma genitalium and Haemophilus influenzae) are available. A comparison of the amino acid sequence for all proteins encoded by the genome of these two distant microorganisms led to the identification of highly homologous proteins. An analysis of these homologous proteins allowed to select some promising candidates for the development of universal DNA-based assays for the detection of bacteria. Since the complete nucleotide sequence of several other microbial genomes are presently available in databases, a person skilled in the art could arrive to the same conclusions by comparing genomes sequences other than those of Mycoplasma genitalium and Haemophilus influenzae. The selected tuf gene encodes a protein (EF-Tu) involved in the translation process during protein synthesis. Subsequently, an extensive nucleotide sequence analysis was performed with the tuf gene sequences available in databases as well as with novel tuf sequences which we have determined as described previously. All computer analysis of amino acid and nucleotide sequences were performed by using the GCG programs. Subsequently, optimal PCR primers for the universal amplification of bacteria were selected with the help of the Oligo™ program. The selected primers are degenerated at several nucleotide positions and contain several inosines in order to allow the amplification of all clinically relevant bacterial species (Annex I). Inosine is a nucleotide analog able to specifically bind to any of the four nucleotides A, C, G or T. Degenerated oligonucleotides consist of an oligonucleotide mix having two or more of the four nucleotides A, C, G or T at the site of mismatches. The inclusion of inosine and/or of degenerescences in the amplification primers allow mismatch tolerance thereby permitting the amplification of a wider array of target nucleotide sequences (Dieffenbach and Dveksler, 1995 PCR Primer: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Plainview, N.Y.).

[0095] The amplification conditions with the universal primers were identical to those used for the species- and genus-specific amplification assays except that the annealing temperature was 50° C. instead of 55° C. This universal PCR assay was specific and nearly ubiquitous for the detection of bacteria. The specificity for bacteria was verified by amplifying genomic DNA isolated from the 12 fungal species listed in Table 6 as well as genomic DNA from Leishmania donovani, Saccharomyces cerevisiae and human lymphocytes. None of the above eukaryotic DNA preparations could be amplified by the universal assay, thereby suggesting that this test is specific for bacteria. The ubiquity of the universal assay was verified by amplifying genomic DNAs from 116 reference strains which represent 95 of the most clinically relevant bacterial species. These species have been selected from the bacterial species listed in Tables 4 and 5. We found that 104 of these 116 strains could be amplified. The bacterial species which could not be amplified belong to the following genera: Corynebacterium (11 species) and Stenotrophomonas (1 species). Sequencing of the tuf genes from these bacterial species has been recently performed. This sequencing data has been used to select new universal primers which may be more ubiquitous. These primers are in the process of being tested. We also observed that for several species the annealing temperature had to be reduced to 45° C. in order to get an efficient amplification. These bacterial species include Gemella morbilbrum, Listeria spp. (3 species) and Gardnerella vaginalis. It is important to note that the 95 bacterial species selected from Tables 4 and 5 to test the ubiquity of the universal assay include all of the most clinically relevant bacterial species associated with a variety of human infections acquired in the community or in hospitals (nosocomial infections). The most clinically important bacterial and fungal pathogens are listed in Tables 1 and 2.

[0096] Examples and Annexes

[0097] The following examples and annexes are intended to be illustrative of the various methods and compounds of the invention, rather than limiting the scope thereof.

[0098] The various annexes show the strategies used for the selection of amplification primers from tuf sequences or from the recA gene: (i) Annex I illustrates the strategy used for the selection of the universal amplification primers from tuf sequences. (ii) Annex II shows the strategy used for the selection of the amplification primers specific for the genus Enterococcus from tuf sequences. (iii) Annex III illustrates the strategy used for the selection of the amplification primers specific for the genus Staphylococcus from tuf sequences. (iv) Annex IV shows the strategy used for the selection of the amplification primers specific for the species Candida albicans from tuf sequences. (v) Annex V illustrates the strategy used for the selection of the amplification primers specific for the genus Streptococcus from recA sequences. (vi) Annex VI gives a list of all selected primer pairs. As shown in these annexes, the selected amplification primers may contain inosines and/or degenerescences. Inosine is a nucleotide analog able to specifically bind to any of the four nucleotides A, C, G or T. Alternatively, degenerated oligonucleotides which consist of an oligonucleotide mix having two or more of the four nucleotides A, C, G or T at the site of mismatches were used. The inclusion of inosine and/or of degenerescences in the amplification primers allow mismatch tolerance thereby permitting the amplification of a wider array of target nucleotide sequences (Dieffenbach and Dveksler, 1995 PCR Primer: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Plainview, N.Y.).

EXAMPLES Example 1

[0099] Selection of Universal PCR Primers from Tuf Sequences.

[0100] As shown in Annex I, the comparison of tuf sequences from a variety of bacterial and eukaryotic species allowed the selection of PCR primers which are universal for the detection of bacteria. The strategy used to design the PCR primers was based on the analysis of a multiple sequence alignment of various tuf sequences. This multiple sequence alignment includes tuf sequences from 38 bacterial species and 3 eukaryotic species either determined by us or selected from databases (Table 13). A careful analysis of this multiple sequence alignment allowed the selection of primer sequences which are conserved within eubacteria but which discriminate sequences from eukaryotes, thereby permitting the universal detection of bacteria. As shown in Annex I, the selected primers contain several inosines and degenerescences. This was necessary because there is a relatively high polymorphism among bacterial tufsequences despite the fact that this gene is highly conserved. In fact, among the tuf sequences that we determined, we found many nucleotide variations as well as some deletions and/or insertions of amino acids. The selected universal primers were specific and ubiquitous for bacteria (Table 7). Of the 95 most clinically important bacterial species tested, 12 were not amplified. These species belong to the genera Corynebacterium (11 species) and Stenotrophomonas (1 species). The universal primers did not amplify DNA of non-bacterial origin, including human and other types of eukaryotic DNA.

Example 2

[0101] Selection of Genus-Specific PCR Primers from Tuf Sequences.

[0102] As shown in Annexes 2 and 3, the comparison of tuf sequences from a variety of bacterial species allowed the selection of PCR primers specific for Enterococcus spp. or for Staphylococcus spp. The strategy used to design the PCR primers was based on the analysis of a multiple sequence alignment of various tuf sequences. These multiple sequence alignments include the tufsequences of four representative bacterial species selected from each target genus as well as tuf sequences from species of other closely related bacterial genera. A careful analysis of those alignments allowed the selection of oligonucleotide sequences which are conserved within the target genus but which discriminate sequences from other closely related genera, thereby permitting the genus-specific and ubiquitous detection and identification of the target bacterial genus.

[0103] For the selection of primers specific for Enterococcus spp. (Annex II), we have sequenced a portion of approximately 890 bp of the tuf genes for Enterococcus avium, E. faecalis, E. faecium and E. gallinarum. All other tufsequences used in the alignment were either sequenced by us or selected from databases. The analysis of this sequence alignment led to the selection of a primer pair specific and ubiquitous for Enterococcus spp. (Table 7). All of the 11 enterococcal species tested were efficiently amplified and there was no amplification with genomic DNA from bacterial species of other genera.

[0104] For the selection of primers specific for Staphylococcus spp. (Annex III), we have also sequenced a portion of approximately 890 bp of the tuf genes for Staphylococcus aureus, S. epidermidis, S. saprophyticus and S. simulans. All other tuf sequences used in the alignment were either sequenced by us or selected from databases. The analysis of this sequence alignment led to the selection of two primer pairs specific and ubiquitous for Staphylococcus spp. (Table 7). Annex III shows the strategy used to select one of these two PCR primer pairs. The same strategy was used to select the other primer pair. Of the 14 staphylococcal species tested, one (S. sciun) could not be amplified by the Staphylococcus-specific PCR assays using either one of these two primer pairs. For PCR assays using either one of these two primer pairs, there was no amplification with DNA from species of other bacterial genera.

Example 3

[0105] Selection from Tuf Sequences of PCR Primers Specific for Candida albicans.

[0106] As shown in Annex IV, the comparison of tuf sequences from a variety of bacterial and eukaryotic species allowed the selection of PCR primers specific for Candida albicans. The strategy used to design the PCR primers was based on the analysis of a multiple sequence alignment of various tuf sequences. This multiple sequence alignment includes tuf sequences of five representative fungal species selected from the genus Candida which were determined by our group (i.e. C. albicans, C. glabrata, C. krusei, C. parapsilosis and C. tropicalis) as well as tuf sequences from other closely related fungal species. tuf sequences from various bacterial species were also included. A careful analysis of this sequence alignment allowed the selection of primers from the C. albicans tuf sequence; these primers discriminate sequences from other closely related Candida species and other fungal species, thereby permitting the species-specific and ubiquitous detection and identification of C. albicans (Table 7). All of 88 Candida albicans strains tested were efficiently amplified and there was no amplification with genomic DNA from other fungal or bacterial species.

Example 4

[0107] Selection of PCR Primers Specific for Streptococcus from recA.

[0108] As shown in Annex V, the comparison of the various bacterial recA gene sequences available from databases (GenBank and EMBL) was used as a basis for the selection of PCR primers which are specific and ubiquitous for the bacterial genus Streptococcus. Since sequences of the recA gene are available for many bacterial species including five species of streptococci, it was possible to choose sequences well conserved within the genus Streptococcus but distinct from the recA sequences for other bacterial genera. When there were mismatches between the recA gene sequences from the five Streptococcus species, an inosine residue was incorporated into the primer (Annex V). The selected primers, each containing one inosine and no degenerescence, were specific and ubiquitous for Streptococcus species (Table 7). This PCR assay amplified all of the 22 streptococcal species tested. However, the Streptococcus-specific assay did not amplify DNA from 3 out of 9 strains of S. mutans and 1 out of 3 strains of S. salivarius. There was no amplification with genomic DNA from other bacterial genera (Table 7).

Example 5

[0109] Nucleotide Sequencing of DNA Fragments.

[0110] The nucleotide sequence of a portion of the tuf genes from a variety of bacterial or fungal species was determined by using the dideoxynucleotide chain termination sequencing method (Sanger et al., 1977, Proc. Natl. Acad. Sci. USA. 74:5463-5467). The sequencing was performed by using an Applied Biosystems automated DNA sequencer (model 373A) with their PRISM™ Sequenase® Terminator Double-stranded DNA Sequencing Kit (Perkin-Elmer Corp., Applied Biosystems Division, Foster City, Calif.). The sequencing strategy does not discriminate tufA and tufB genes because the sequencing primers hybridize efficiently to both bacterial tuf genes. These DNA sequences are shown in the sequence listing (SEQ ID Nos: 118 to 146). The presence of several degenerated nucleotides in the various tuf sequences determined by our group (Table 13) corresponds to sequence variations between tufA and tufB.

[0111] Oligonucleotide Primers and Probes Selection.

[0112] Oligonucleotide probes and amplification primers were selected from the given proprietary DNA fragments or database sequences using the Oligo™ program and were synthesized with an automated ABI DNA synthesizer (Model 391, Perkin-Elmer Corp., Applied Biosystems Division) using phosphoramidite chemistry.

Example 6

[0113] Labeling of Oligonucleotides for Hybridization Assays.

[0114] Each oligonucleotide was 5′ end-labeled with y-³²P (dATP) by the T4 polynucleotide kinase (Pharmacia) as described earlier. The label could also be non-radioactive.

[0115] Specificity Test for Oligonucleotide Probes.

[0116] All labeled oligonucleotide probes were tested for their specificity by hybridization to DNAs from a variety of bacterial and fungal species selected from Tables 4, 5 and 6 as described earlier. Species-specific or genus-specific probes were those hybridizing only to DNA from the microbial species or genus from which it was isolated. Oligonucleotide probes found to be specific were submitted to ubiquity tests as follows.

[0117] Ubiquity Test for Oligonucleotide Probes.

[0118] Specific oligonucleotide probes were then used in ubiquity tests with strains of the target species or genus including reference strains and other strains obtained from various countries and which are representative of the diversity within each target species or genus. Chromosomal DNAs from the isolates were transferred onto nylon membranes and hybridized with labeled oligonucleotide probes as described for specificity tests. The batteries of isolates constructed for each target species or genus contain reference ATCC strains as well as a variety of clinical isolates obtained from various sources. Ubiquitous probes were those hybridizing to at least 80% of DNAs from the battery of clinical isolates of the target species or genus.

Example 7

[0119] Same as example 6 except that a pool of specific oligonucleotide probes is used for microbial identification (i) to increase sensitivity and assure 100% ubiquity or (ii) to identify simultaneously more than one microbial species and/or genus. Microbial identification could be performed from microbial cultures or directly from any clinical specimen.

Example 8

[0120] Same as example 6 except that bacteria or fungi were detected directly from clinical samples. Any biological sample was loaded directly onto a dot blot apparatus and cells were lysed in situ for bacterial or fungal detection and identification. Blood samples should be heparizined in order to avoid coagulation interfering with their convenient loading on a dot blot apparatus.

Example 9

[0121] PCR Amplification.

[0122] The technique of PCR was used to increase the sensitivity and the rapidity of the assays. The sets of primers were tested in PCR assays performed directly from bacterial colonies or from a standardized bacterial suspension (see Example 10) to determine their specificity and ubiquity (Table 7). Examples of specific and ubiquitous PCR primer pairs are listed in Annex VI.

[0123] Specificity and Ubiquity Tests for Amplification Primers.

[0124] The specificity of all selected PCR primer pairs was tested against DNAs from a variety of bacterial and fungal species selected from Tables 4, 5 and 6 as described earlier. Primer pairs found specific for each species or genus were then tested for their ubiquity to ensure that each set of primers could amplify at least 90% of DNAs from a battery of isolates of the target species or genus. The batteries of isolates constructed for each species contain reference ATCC strains and various clinical isolates from around the world which are representative of the diversity within each species or genus.

[0125] Standard precautions to avoid false positive PCR results should be taken (Kwok and Higuchi, 1989, Nature, 239:237-238). Methods to inactivate PCR amplification products such as the inactivation by uracil-N-glycosylase may be used to control PCR carryover.

Example 10

[0126] Amplification Directly from Bacterial or Yeast Cultures.

[0127] PCR assays were performed either directly from a bacterial colony or from a bacterial suspension, the latter being adjusted to a standard McFarland 0.5 (corresponds to approximately 1.5×10⁸ bacteria/mL). In the case of direct amplification from a colony, a portion of a colony was transferred using a plastic rod directly into a 20 μL PCR reaction mixture containing 50 mM KCl, 10 mM Tris-HCl (pH 9.0), 0.1% Triton X-100, 2.5 mM MgCl₂, 0.4 μM of each primer, 200 μM of each of the four dNTPs and 0.5 unit of Taq DNA polymerase (Promega) combined with the TaqStart™ antibody (Clontech Laboratories Inc.). For the bacterial suspension, 1 μL of the cell suspension was added to 19 μL of the same PCR reaction mixture. For the identification from yeast cultures, 1 μL of a standard McFarland 1.0 (corresponds to approximately 3.0×10⁸ bacteria/mL) concentrated 100 times by centrifugation was added directly to the PCR reaction. This concentration step for yeast cells was performed because a McFarland 0.5 for yeast cells has approximately 200 times fewer cells than a McFarland 0.5 for bacterial cells.

[0128] PCR reactions were then subjected to thermal cycling (3 min at 95° C. followed by 30 cycles of 1 second at 95° C. for the denaturation step and 30 seconds at 55° C. for the annealing-extension step) using a PTC-200 thermal cycler. PCR amplification products were then analyzed by standard agarose gel (2%) electrophoresis. Amplification products were visualized in agarose gels containing 0.25 μg/mL of ethidium bromide under UV at 254 nm. The entire PCR assay can be completed in approximately one hour.

[0129] Primer sequences derived from highly conserved regions of the bacterial 16S ribosomal RNA gene were used to provide an internal control for all PCR reactions. Alternatively, the internal control was derived from sequences not found in microorganisms or in the human genome. The internal control was integrated into all amplification reactions to verify the efficiency of the PCR assays and to ensure that significant PCR inhibition was absent. The internal control derived from rRNA was also useful to monitor the efficiency of the bacterial lysis protocols. The internal control and the species-specific or genus-specific amplifications were performed simultaneously in multiplex PCR assays.

Example 11

[0130] Amplification Directly from Urine Specimens.

[0131] For PCR amplification performed directly from urine specimens, 1 μL of urine was mixed with 4 μL of a lysis solution containing 500 mM KCl, 100 mM tris-HCl (pH 9.0), 1% triton X-100. After incubation for at least 15 minutes at room temperature, 1 μL of the treated urine specimen was added directly to 19 μL of the PCR reaction mixture. The final concentration of the PCR reagents was 50 mM KCl, 10 mM Tris (pH 9.0), 0.1% Triton X-100, 2.5 mM MgCl₂, 0.4 μM of each primer, 200 μM of each of the four dNTPs. In addition, each 20 μL reaction contained 0.5 unit of Taq DNA polymerase (Promega) combined with the TaqStart™ antibody (Clontech Laboratories Inc.).

[0132] Strategies for the internal control, PCR amplification and agarose gel detection of the amplicons are as previously described in example 10.

Example 12

[0133] Detection of Antibiotic Resistance Genes.

[0134] The presence of specific antibiotic resistance genes which are frequently encountered and clinically relevant is identified using the PCR amplification or hybridization protocols described previously. Specific oligonucleotides used as a basis for the DNA-based tests are selected from the antibiotic resistance gene sequences. These tests, which allow the rapid evaluation of bacterial resistance to antimicrobial agents, can be performed either directly from clinical specimens, from a standardized bacterial suspension or from a bacterial colony and should complement diagnostic tests for the universal detection of bacteria as well as for the species-specific and genus-specific microbial detection and identification.

Example 13

[0135] Same as examples 10 and 11 except that assays were performed by multiplex PCR (i.e. using several pairs of primers in a single PCR reaction) to reach an ubiquity of 100% for the specific targeted pathogen(s). For more heterogeneous microbial species or genus, a combination of PCR primer pairs may be required to detect and identify all representatives of the target species or genus.

[0136] Multiplex PCR assays could also be used to (i) detect simultaneously several microbial species and/or genera or, alternatively, (ii) to simultaneously detect and identify bacterial and/or fungal pathogens and detect specific antibiotic resistance genes either directly from a clinical specimen or from bacterial cultures.

[0137] For these applications, amplicon detection methods should be adapted to differentiate the various amplicons produced. Standard agarose gel electrophoresis could be used because it discriminates the amplicons based on their sizes. Another useful strategy for this purpose would be detection using a variety of fluorescent dyes emitting at different wavelengths. The fluorescent dyes can be each coupled with a specific oligonucleotide linked to a fluorescence quencher which is degraded during amplification to release the fluorescent dyes (e.g. TaqMan™, Perkin Elmer).

Example 14

[0138] Detection of Amplification Products.

[0139] The person skilled in the art will appreciate that alternatives other than standard agarose gel electrophoresis (Example 10) may be used for the revelation of amplification products. Such methods may be based on fluorescence polarization or on the detection of fluorescence after amplification (e.g. Amplisensor™, Biotronics; TaqMan™, Perkin-Elmer Corp.) or other labels such as biotin (SHARP Signal™ system, Digene Diagnostics). These methods are quantitative and may be automated. One of the amplification primers or an internal oligonucleotide probe specific to the amplicon(s) derived from the species-specific, genus-specific or universal DNA fragments is coupled with the fluorescent dyes or with any other label. Methods based on the detection of fluorescence are particularly suitable for diagnostic tests since they are rapid and flexible as fluorescent dyes emitting at different wavelengths are available.

Example 15

[0140] Species-specific, genus-specific, universal and antibiotic resistance gene amplification primers can be used in other rapid amplification procedures such as the ligase chain reaction (LCR), transcription-mediated amplification (TMA), self-sustained sequence replication (3SR), nucleic acid sequence-based amplification (NASBA), strand displacement amplification (SDA), cycling probe technology (CPT) and branched DNA (bDNA) or any other methods to increase the sensitivity of the test. Amplifications can be performed from isolated bacterial cultures or directly from any clinical specimen. The scope of this invention is therefore not limited to the use of the DNA sequences from the enclosed Sequence Listing for PCR only but rather includes the use of any procedures to specifically detect bacterial DNA and which may be used to increase rapidity and sensitivity of the tests.

Example 16

[0141] A test kit would contain sets of probes specific for each microbial species or genus as well as a set of universal probes. The kit is provided in the form of test components, consisting of the set of universal probes labeled with non-radioactive labels as well as labeled species- or genus-specific probes for the detection of each pathogen of interest in specific types of clinical samples. The kit will also include test reagents necessary to perform the pre-hybridization, hybridization, washing steps and hybrid detection. Finally, test components for the detection of known antibiotic resistance genes (or derivatives therefrom) will be included. Of course, the kit will include standard samples to be used as negative and positive controls for each hybridization test.

[0142] Components to be included in the kits will be adapted to each specimen type and to detect pathogens commonly encountered in that type of specimen. Reagents for the universal detection of bacteria will also be included. Based on the sites of infection, the following kits for the specific detection of pathogens may be developed:

[0143] A kit for the universal detection of bacterial or fungal pathogens from all clinical specimens which contains sets of probes specific for highly conserved regions of the microbial genomes.

[0144] A kit for the detection of microbial pathogens retrieved from urine samples, which contains 5 specific test components (sets of probes for the detection of Enterococcus faecium, Enteroccus species, Staphylococcus saprophyticus, Staphylococcus species and Candida albicans).

[0145] A kit for the detection of respiratory pathogens which contains 3 specific test components (sets of probes for the detection of Staphylococcus species, Enterococcus species and Candida albicans).

[0146] A kit for the detection of pathogens retrieved from blood samples, which contains 10 specific test components (sets of probes for the detection of Streptococcus species, Streptococcus agalactiae, Staphylococcus species, Staphylococcus saprophyticus, Enterococcus species, Enterococcus faecium, Neisseria species, Neisseria meningitidis, Listeria monocytogenes and Candida albicans). This kit can also be applied for direct detection and identification from blood cultures.

[0147] A kit for the detection of pathogens causing meningitis, which contains 5 specific test components (sets of probes for the detection of Streptococcus species, Listeria monocytogenes, Neisseria meningitidis, Neisseria species and Staphylococcus species).

[0148] A kit for the detection of clinically important antibiotic resistance genes which contains sets of probes for the specific detection of at least one of the 26 following genes associated with antibiotic resistance: bla_(tem), bla_(rob), bla_(shv), bla_(oxa), blaZ, aadB, aacC1, aacC2, aacC3, aacA4, aac6′-lla, ermA, ermB, ermC, mecA, vanA, vanb, vanC, satA, aac(6′)-aph(2″), aad(6′), vat, vga, msrA, sul and int.

[0149] Other kits adapted for the detection of pathogens from skin, abdominal wound or any other clinically relevant infections may also be developed.

Example 17

[0150] Same as example 16 except that the test kits contain all reagents and controls to perform DNA amplification assays. Diagnostic kits will be adapted for amplification by PCR (or other amplification methods) performed directly either from clinical specimens or from microbial cultures. Components required for (i) universal bacterial detection, (ii) species-specific and genus-specific bacterial and/or fungal detection and identification and (iii) detection of antibiotic resistance genes will be included.

[0151] Amplification assays could be performed either in tubes or in microtitration plates having multiple wells. For assays in plates, the wells will contain the specific amplification primers and control DNAs and the detection of amplification products will be automated. Reagents and amplification primers for universal bacterial detection will be included in kits for tests performed directly from clinical specimens. Components required for species-specific and genus-specific bacterial and/or fungal detection and identification as well as for the simultaneous antibiotic resistance genes detection will be included in kits for testing directly from bacterial or fungal cultures as well as in kits for testing directly from any type of clinical specimen.

[0152] The kits will be adapted for use with each type of specimen as described in example 16 for hybridization-based diagnostic kits.

Example 18

[0153] It is understood that the use of the probes and amplification primers described in this invention for bacterial and/or fungal detection and identification is not limited to clinical microbiology applications. In fact, we feel that other sectors could also benefit from these new technologies. For example, these tests could be used by industries for quality control of food, water, air, pharmaceutical products or other products requiring microbiological control. These tests could also be applied to detect and identify bacteria or fungi in biological samples from organisms other than humans (e.g. other primates, birds, plants, mammals, farm animals, livestock and others). These diagnostic tools could also be very useful for research purposes including clinical trials and epidemiological studies.

[0154] This invention has been described herein above, and it is readily apparent that modifications can be made thereto without departing from the spirit of this invention. These modifications are under the scope of this invention, as defined in the appended claims. TABLE 1 Distribution (%) of nosocomial pathogens for various human infections in USA (1990-1992)¹. Pathogen UTI² SSI³ BSI⁴ Pneumonia CSF⁵ Escherichia coil 27 9 5 4 2 Staphylococcus aureus 2 21 17 21 2 Staphylococcus epidermidis 2 6 20 0 1 Enterococcus faecalis 16 12 9 2 0 Enterococcus faecium 1 1 0 0 0 Pseudomonas aeruginosa 12 9 3 18 0 Klebsiella pneumoniae 7 3 4 9 0 Proteus mirabilis 5 3 1 2 0 Streptococcus pneumoniae 0 0 3 1 18 Group B Streptococci 1 1 2 1 6 Other Streptococci 3 5 2 1 3 Haemophilus influenzae 0 0 0 6 45 Neisseria meningitidis 0 0 0 0 14 Listeria monocytogenes 0 0 0 0 3 Other Enterococci 1 1 0 0 0 Other Staphylococci 2 8 13 20 Candida albicans 9 3 5 5 0 Other Candida 2 1 3 10 Enterobacter spp. 5 7 4 12 2 Acinetobacter spp. 1 1 2 4 2 Citrobacter spp. 2 1 1 1 0 Serratia marcescens 1 1 1 3 1 Other Klebsiella 1 1 1 2 1 Others 0 6 4 5 0

[0155] TABLE 2 Distribution (%) of bloodstream infection pathogens in Quebec (1995), Canada (1992), UK (1969-1988) and USA (1990-1992). UK³ USA⁴ Que- Ca- Community- Hospital- Hospital- Organism bec¹ nada² acquired acquired acquired E. coil 15.6 53.8 24.8 20.3  5.0 S. epidermidis 25.8 NI⁶  0.5  7.2 31.0 and other CoNS⁵ S. aureus  9.6 NI  9.7 19.4 16.0 S. pneumoniae  6.3 NI 22.5  2.2 NR⁷ E. faecalis  3.0 NI  1.0  4.2 NR E. faecium  2.6 NI  0.2  0.5 NR Enterococcus NR NI NR NR  9.0 spp. H. influenzae  1.5 NR  3.4  0.4 NR P. aeruginosa  1.5  8.2  1.0  8.2  3.0 K. pneumoniae  3.0 11.2  3.0  9.2  4.0 P. mirabilis NR  3.9  2.8  5.3  1.0 S. pyogenes NR NI  1.9  0.9 NR Enterobacter spp.  4.1  5.5  0.5  2.3  4.0 Candida spp.  8.5 NI NR  1.0  8.0 Others 18.5 17.4⁸ 28.7 18.9 19.0

[0156] TABLE 3 Distribution of positive and negative clinical specimens tested at the microbiology laboratory of the CHUL (February 1994-January 1995). Clinical specimens No. of samples % of positive % of negative and/or sites tested (%) specimens specimens Urine 17,981 (54.5) 19.4 80.6 Blood culture/marrow 10,010 (30.4) 6.9 93.1 Sputum  1,266 (3.8) 68.4 31.6 Superficial pus  1,136 (3.5) 72.3 27.7 Cerebrospinal fluid   553 (1.7) 1.0 99.0 Synovial fluid   523 (1.6) 2.7 97.3 Respiratory tract   502 (1.5) 56.6 43.4 Deep pus   473 (1.4) 56.8 43.2 Ears   289 (0.9) 47.1 52.9 Pleural and pericardial   132 (0.4) 1.0 99.0 fluid Peritoneal fluid   101 (0.3) 28.6 71.4 Total: 32,966 (100.0) 20.0 80.0

[0157] TABLE 4 Gram-negative bacterial species (90) used to test the specificity of PCR primers and DNA probes (continues on next page). Number of Number of reference reference strains strains Bacterial species tested^(a) Bacterial species tested^(a) Acinetobacter baumannii 1 Moraxella phenylpyruvica 1 Acinetobacter Iwoffii 3 Morganella morganii 1 Actinobacillus lignieresii 1 Neisseria animalis 1 Alcaligenes faecalis 1 Neisseria canis 1 Alcaligenes odorans 1 Neisseria caviae 1 Alcaligenes xylosoxydans Neisseria cinerea 1 subsp. denitrificans 1 Neisseria cuniculi 1 Bacteroides distasonis 1 Neisseria elongata 1 subsp. elongata Bacteroides fragilis 1 Neisseria elongata 1 subsp. glycoytica Bacteroides ovatus 1 Neisseria flavescens 1 Bacteroides 1 Neisseria flavescens 1 thetaiotaomicron Branham Bacteroides vulgatus 1 Neisseria gonorrhoeae 18 Bordetella bronchiseptica 1 Neisseria lactamica 1 Bordetella parapertussis 1 Neisseria meningitidis 4 Bordetella pertussis 2 Neisseria mucosa 2 Burkholderia cepacia 1 Neisseria polysaccharea 1 Citrobacter amalonaticus 1 Neisseria sicca 3 Citrobacter diversus 2 Neisseria subflava 3 subsp. koseri Citrobacter freundii 1 Neisseria weaveri 1 Comamonas acidovorans 1 Ochrobactrum antropi 1 Enterobacter aerogenes 1 Pasteurella aerogenes 1 Enterobacter 1 Pasteurella multocida 1 agglomerans Enterobacter cloacae 1 Prevotella melaninogenica 1 Escherichia coli 9 Proteus mirabilis 3 Escherichia fergusonii 1 Proteus vulgaris 1 Escherichia hermannii 1 Providencia alcalifaciens 1 Escherichia vulneris 1 Providencia rettgeri 1 Flavobacterium 1 Providencia rustigianii 1 meningosepticum Flavobacterium 1 Providencia stuartii 1 indologenes Flavobacterium odoratum 1 Pseudomonas aeruginosa 14 Fusobacterium 2 Pseudomonas fluorescens 2 necrophorum Gardnerella vaginalis 1 Pseudomonas stutzeri 1 Haemophilus 1 Salmonella arizonae 1 haemolyticus Haemophilus influenzae 12 Salmonella choleraesuis 1 Haemophilus 1 Salmonella gallinarum 1 parahaemolyticus Haemophilus 2 Salmonella typhimurium 3 parainfluenzae Hafnia alvei 1 Serratia liquefaciens 1 Kingella indologenes 1 Serratia marcescens 1 subsp. suttonella Kingella kingae 1 Shewanella putida 1 Klebsiella ornithinolytica 1 Shigella boydii 1 Klebsiella oxytoca 1 Shigella dysenteriae 1 Klebsiella pneumoniae 8 Shigella flexneri 1 Moraxella atlantae 1 Shigella sonnei 1 Moraxella catarrhalis 5 Stenotrophomonas 1 maltophilia Moraxella lacunata 1 Yersinia enterocolitica 1 Moraxella osloensis 1

[0158] TABLE 5 Gram-positive bacterial species (97) used to test the specificity of PCR primers and DNA probes (continues on next page). Number of Number of reference reference strains strains Bacterial species tested^(a) Bacterial species tested^(a) Abiotrophia adiacens 1 Micrococcus kristinae 1 Abiotrophia defectiva 1 Micrococcus luteus 1 Actinomyces israelii 1 Micrococcus lylae 1 Clostridium perfringens 1 Micrococcus roseus 1 Corynebacterium accolens 1 Micrococcus varians 1 Corynebacterium 1 Peptococcus niger 1 aquaticum Corynebacterium bovis 1 Peptostreptococcus 1 anaerobius Corynebacterium cervicis 1 Peptostreptococcus 1 asaccharolyticus Corynebacterium 6 Staphylococcus aureus 10  diphteriae Corynebacterium 1 Staphylococcus auricularis 1 flavescens Corynebacterium 6 Staphylococcus capitis 1 genitalium subsp. urealyticus Corynebacterium jeikeium 1 Staphylococcus cohnii 1 Corynebacterium kutcheri 1 Staphylococcus epidermidis 2 Corynebacterium 1 Staphylococcus 2 matruchotii haemolyticus Corynebacterium 1 Staphylococcus hominis 2 minutissimum Corynebacterium 1 Staphylococcus 1 mycetoides lugdunensis Corynebacterium 1 Staphylococcus 3 pseudodiphtheriticum saprophyticus Corynebacterium 6 Staphylococcus schleiferi 1 pseudogenitalium Corynebacterium renale 1 Staphylococcus sciuri 1 Corynebacterium striatum 1 Staphylococcus simulans 1 Corynebacterium ulcerans 1 Staphylococcus warneri 1 Corynebacterium 1 Staphylococcus xylosus 1 urealyticum Corynebacterium xerosis 1 Streptococcus agalactiae 6 Enterococcus avium 1 Streptococcus anginosus 2 Enterococcus 1 Streptococcus bovis 2 casseliflavus Enterococcus cecorum 1 Streptococcus constellatus 1 Enterococcus dispar 1 Streptococcus crista 1 Enterococcus durans 1 Streptococcus dysgalactiae 1 Enterococcus faecalis 6 Streptococcus equi 1 Enterococcus faecium 3 Streptococcus gordonii 1 Enterococcus flavescens 1 Group C Streptococci 1 Enterococcus gallinarum 3 Group D Streptococci 1 Enterococcus hirae 1 Group E Streptococci 1 Enterococcus mundtii 1 Group F Streptococci 1 Enterococcus 1 Group G Streptococci 1 pseudoavium Enterococcus raffinosus 1 Streptococcus intermedius 1 Enterococcus 1 Streptococcus mitis 2 saccharolyticus Enterococcus solitarius 1 Streptococcus mutans 1 Eubacterium lentum 1 Streptococcus oralis 1 Gemella haemolysans 1 Streptococcus parasanguis 1 Gemella morbillorum 1 Streptococcus pneumoniae 6 Lactobacillus acidophilus 1 Streptococcus pyogenes 3 Listeria innocua 1 Streptococcus salivarius 2 Listeria ivanovii 1 Streptococcus sanguis 2 Listeria grayi 1 Streptococcus sobrinus 1 Listeria monocytogenes 3 Streptococcus suis 1 Listeria murrayi 1 Streptococcus uberis 1 Listeria seeligeri 1 Streptococcus vestibularis 1 Listeria welshimeri 1

[0159] TABLE 6 Fungal species (12) used to test the specificity of PCR primers and DNA probes. Number of reference Fungal species strains tested^(a) Candida albicans 12 Candida glabrata 1 Candida guilliermondii 1 Candida kefyr 3 Candida krusei 2 Candida lusitaniae 1 Candida parapsilosis 2 Candida tropicalis 3 Rhodotorula glutinis 1 Rhodotorula minuta 1 Rhodotorula rubra 1 Saccharomyces cerevisiae 1

[0160] TABLE 7 PCR assays developed for several clinically important bacterial and fungal pathogens (continues on next page). Primer Pair^(a) Amplicon DNA amplification from Organism SEQ ID NO size (bp) Ubiquity^(b) culture^(c) specimens^(d) Enterococcus faecium 1-2 216 79/80 + + Listeria monocytogenes 3-4 130 164/168^(e) + + Neisseria meningitidis 5-6 177 258/258 + + Staphylococcus 7-8 149 245/260 + NT saprophyticus Streptococcus  9-10 154 29/29 + + agalactiae Candida albicans 11-12 149 88/88 + NT Enterococcus 13-14 112 87/87 + NT spp. (11 species)^(f) Neisseria spp. 15-16 103 321/321 + + (12 species)^(f) Staphylococcus spp. 17-18 192 13/14 + NT (14 species) 19-20 221 13/14 + NT Streptococcus spp. 21-22 153  210/214^(g) + + (22 species)^(f) Universal detection^(h) 23-24 309  104/116^(i) + + (95 species)^(i) # genus-specific PCR assay, except for the Staphylococcus-specific assay, which does not amplify S. sciuri.

[0161] TABLE 8 Target genes for the various genus-specific, species-specific and universal amplification assays. Microorganisms Gene Protein encoded Candida albicans tuf translation elongation factor EF-Tu Enterococcus faecium ddl D-alanine:D-alanine ligase Listeria monocytogenes actA actin-assembly inducing protein Neisseria meningitidis omp outer membrane protein Streptococcus agalactiae cAMP cAMP factor Staphylococcus unknown unknown saprophyticus Enterococcus spp. tuf translation elongation factor EF-Tu Neisseria spp. asd ASA-dehydrogenase Staphylococcus spp. tuf translation elongation factor EF-Tu Streptococcus spp. recA RecA protein Universal detection tuf translation elongation factor EF-Tu

[0162] TABLE 9 Antibiotic resistance genes selected for diagnostic purposes. SEQ ID NOs selected originating Genes primers fragment Antibiotics Bacteria^(a) bla_(oxa)  49-50 110 β-lactams Enterobacteriaceae, Pseudomonadaceae blaZ  51-52 111 β-lactams Enterococcus spp. aac6′-lla  61-64 112 Aminoglycosides Pseudomonadaceae ermA  91-92 113 Macrolides Staphylococcus spp. ermB  93-94 114 Macrolides Staphylococcus spp. ermC  95-96 115 Macrolides Staphylococcus spp. vanB  71-74 116 Vancomycin Enterococcus spp. vanC  75-76 117 Vancomycin Enterococcus spp. aad(6′) 173-174 — Streptomycin Enterococcus spp.

[0163] TABLE 10 Antibiotic resistance genes from our co-pending U.S. patent applications (N.S. 08/526840) and PCT (PCT/CA/95/00528) for which we have selected PCR primer pairs. SEQ ID NOs Genes of selected primers Antibiotics Bacteria^(a) bla_(tem)  37-40 β-lactams Enterobacteriaceae, Pseudomonadaceae, Haemophilus spp., Neisseria spp. bla_(rob)  45-48 β-lactams Haemophilus spp., Pasteurella spp. bla_(shv)  41-44 β-lactams Kiebsiella spp. and other Enterobacteriaceae aadB  53-54 Aminoglycosides Enterobacteriaceae, aacC1  55-56 Pseudomonadaceae aacC2  57-58 aacC3  59-60 aacA4  65-66 mecA  97-98 β-lactams Staphylococcus spp. vanA  67-70 Vancomycin Enterococcus spp. satA  81-82 Macrolides Enterococcus spp. aac(6′)-aph(2″)  83-86 Aminoglycosides Enterococcus spp., Staphylococcus spp. vat  87-88 Macrolides Staphylococcus spp. vga  89-90 Macrolides Staphylococcus spp. msrA  77-80 Erythromycin Staphylococcus spp. int  99-102 β-lactams, Enterobacteriaceae, trimethoprim, sul 103-106 aminoglycosides, Pseudomonadaceae antiseptic, chloramphenicol

[0164] TABLE 11 Correlation between disk diffusion and PCR amplification of antibiotic resistance genes in Staphylococcus species^(a). Pheno- Disk diffusion (Kirby-Bauer)^(b) Antibiotic type PCR Resistant Intermediate Sensitive Penicillin blaZ + 165 0 0 − 0 0 31 Oxacillin mecA + 51 11 4 − 2 0 128 Gentamycin aac(6′) + 24 18 6 aph(2″) − 0 0 148 Erythromycin ermA + 15 0 0 ermB + 0 0 0 ermC + 43 0 0 msrA + 4 0 0 − 0 1 136

[0165] TABLE 12 Correlation between disk diffusion profiles and PCR amplification of antibiotic resistance genes in Enterococcus species^(a). Disk diffusion (Kirby-Bauer)^(b) Antibiotic Phenotype PCR Resistant Sensitive Ampicillin blaZ + 0 2 − 1 30 Gentamycin aac(6′)aph(2″) + 51 1 − 3 38 Streptomycin aad(6′) + 26 15 − 6 27 Vancomycin vanA + 36 0 vanB + 26 0 − 0 40

[0166] TABLE 13 Origin of tuf sequences in the Sequence Listing (continues on next page). SEQ ID NO Bacterial or fungal species Source 118 Abiotrophia adiacens This patent 119 Abiotrophia defectiva ″ 120 Candida albicans ″ 121 Candida glabrata ″ 122 Candida krusei ″ 123 Candida parapsilosis ″ 124 Candida tropicalis ″ 125 Corynebacterium accolens ″ 126 Corynebacterium diphteriae ″ 127 Corynebacterium genitalium ″ 128 Corynebacteriun jeikeium ″ 129 Corynebacterium ″ pseudotuberculosis 130 Corynebacterium striatum ″ 131 Enterococcus avium ″ 132 Enterococcus faecalis ″ 133 Enterococcus faecium ″ 134 Enterococcus gallinarum ″ 135 Gardnerella vaginalis ″ 136 Listeria innocua ″ 137 Listeria ivanovii ″ 138 Listeria monocytogenes ″ 139 Listeria seeligeri ″ 140 Staphylococcus aureus ″ 141 Staphylococcus epidermidis ″ 142 Staphylococcus saprophyticus ″ 143 Staphylococcus simulans ″ 144 Streptococcus agalactiae ″ 145 Streptococcus pneumoniae ″ 146 Streptococcus salivarius ″ 147 Agrobacterium tumefaciens Database 148 Bacillus subtilis ″ 149 Bacteroides fragilis ″ 150 Borrelia burgdorferi ″ 151 Brevibacterium linens ″ 152 Burkholderia cepacia ″ 153 Chlamydia trachomatis ″ 154 Escherichia coli ″ 155 Fibrobacter succinogenes ″ 156 Flavobacterium ferrugineum ″ 157 Haemophilus influenzae ″ 158 Helicobacter pylori ″ 159 Micrococcus luteus ″ 160 Mycobacterium tuberculosis ″ 161 Mycoplasma genitalium ″ 162 Neisseria gonorrhoeae ″ 163 Rickettsia prowazekii ″ 164 Salmonella typhimurium ″ 165 Shewanella putida ″ 166 Stigmatella aurantiaca ″ 167 Streptococcus pyogenes ″ 168 Thiobacillus cuprinus ″ 169 Treponema pallidum ″ 170 Ureaplasma urealyticum ″ 171 Wolinella succinogenes ″

[0167] Annex I: Strategy for the selection from tuf sequences of the universal amplification primers. SEQ ID NO 491                       517...776                       802 Abiotrophia CA ACTGTAAC   TGGTGTTGAA   ATGTT CC...AA ATGGT   AATGCCTGGT   GATAACGT AA 118 adiacens Abiotrophia CT ACCGTTAC   CGGTGTTGAA   ATGTT CC...AA ATGGT   TATGCCAGGC   GACAACGT AC 119 defectiva Agrobacterium CG ACTGTTAC   CGGCGTTGAA   ATGTT CC...AA ATGGT   TATGCCTGGC   GACAACGT CA 147 tumefaciens Bacillus CA ACTGTTAC   AGGTGTTGAA   ATGTT CC...AA ATGGT   TATGCCTGGA   GATAACA CTG 148 subtilis Bacteroides CAGTTGTAAC   AGGTGTTGAA   ATGTT CC...AA ATGGT   AATGCCGGGT   GATAACGT AA 149 fragilis Borrelia CT ACTGTTAC   TGGTGTTGAA   ATGTT CC...AA ATGGT   TATGCCTGGT   GATAATGT TG 150 burgdorteri Brevibacterium CG ACTGTCAC   CG C T A TCGAG   ATGTT CC...AG ATGGT   CATGCCCGGC   GACA C CA CCG 151 linens Burkholderia CG ACCTGCAC   GGGCGTTGAA   ATGTT CC...AA ATGGT   CATGCCGGGC   GACAACGT GT 152 cepacia Chlamydia CG ATTGTTAC   TGGGGTTGAA   ATGTT CA...AG ATGGT   CATGCCTGGG   GATAACGT TG 153 trachomatis Corynebacterium CC ACCGTTAC   CGGT A TCGAG   ATGTT CC...AG ATGGT   CATGCCTGGC   GACAACGT CG 126 diphteriae Corynebacterium CC ACCGTTAC   C TC C A TCGAG   ATGTT CA...AG ATGGT   TATGCCGGGC   GACAACGT TG 127 genitalium Corynebacterium CC ACCGTTAC   C TC C A TCGAG   ATGTT CA...AG ATGGT   TATGCCGGGC   GACAACGT TG 128 jeikeium Enterococcus CA ACYGTTAC   AGGTGTTGAA   ATGTT CC...AA ATGGT   AATGCCTGGT   GATAACGT TG 132 faecalis Enterococcus CA ACAGTTAC   TGGTGTTGAA   ATGTT CC...AA ATGGT   CATGCCCGGT   GACAACGT .. 133 faecium Escherichia CT ACCTGTAC   TGGCGTTGAA   ATGTT CC...AG ATGGT   AATGCCGGGC   GACAACAT CA 154 coli Fibrobacter ACGT C A TCAC   CGGTGTTGAA   ATGTT CC...AA ATGGT   TA CT CCGGGT   GACA CG GT CA 155 succinogenes Flavobacterium CT ACCGTTAC   AGGTGTTGAG   ATGTT CC...AA ATGGT   TATGCCTGGT   GATAACA CCA 156 ferrugineum Gardnerella CC ACCGTCAC   C TC T A TCGAG   A CC TT CC...AA ATGGT   T CA GCCAGGC   GAT C ACG CAA 135 vaginalis Haemophilus CT ACTGTAAC   GGGTGTTGAA   ATGTT CC...AA ATGGT   AATGCCAGGC   GATAACAT CA 157 influenzea Helicobacter CG ACTGTAAC   CGGTGTAGAA   ATGTT TA...AA ATGGT   TATGCCTGGC   GATAATGT GA 158 pylori Listeria TAGT AGTAAC   TGGAGTAGAA   ATGTT CC...AA ATGGT   AA Y GCCTGGT   GATAACAT TG 138 monocytogenes Micrococcus CC ACTGTCAC   CGGC A TCGAG   ATGTT CC...AG ATGGT   CATGCCCGGC   GACAACA CCG 159 luteus Mycobacterium CC ACCGTCAC   CGGTGTGGAG   ATGTT CC...AG ATGGT   GATGCCCGGT   GACAACA CCA 160 Mycoplasma CAGT TGTTAC   TGGA A TTGAA   ATGTT CA...AA ATGGT   T C T A CCTGGT   GATAATG CTT 161 genitalium Neisseria CC ACCTGTAC   CGGCGTTGAA   ATGTT CC...AA ATGGT   AATGCCGGGT   GAGAACGT AA 162 gonorrhoeae Rickettsia CG ACTTGTAC   AGGTGTAGAA   ATGTT CA...AG ATGGT   TATGCCTGGA   GATAATG CTA 163 prowazekii Salmonella CT ACCTGTAC   TGGCGTTGAA   ATGTT CC...AG ATGGT   AATGCCGGGC   GACAACAT CA 164 typhimurium Shewanella CA ACGTGTAC   TGGTGTAGAA   ATGTT CC...AG ATGGT   AATGCCAGGC   GATAACAT CA 165 putida Stigmatella CGGT C A TCAC   GGGGGTGGAG   ATGTT CC...AG ATGGT   GATGCCGGGA   GACAACAT CG 166 aurantiaca Staphylococcus CA ACTGTTAC   AGGTGTTGAA   ATGTT CC...AA ATGGT   AATGCCTGGT   GATAACGT TG 140 aureus Staphylococcus CA ACTGTTAC   TGGTGTAGAA   ATGTT CC...AA ATGGT   TATGCCTGGC   GACAACGT TG 141 epidermidis Streptococcus CAGT TGTTAC   TGGTGTTGAA   ATGTT CC...AA ATGGT   TATGCCTGGT   GATAACGT TA 144 agalactiae Streptococcus CAGT TGTTAC   TGGTGTTGAA   ATGTT CC...AA ATGGT   AATGCCTGGT   GATAACGT GA 145 pneumoniae Streptococcus CTGT TGTTAC   TGGTGTTGAA   ATGTT CC...AA ATGGT   TATGCCTGGT   GATAACGT GA 167 pyogenes Thiobacillus CC ACCTGCAC   CGGCGTGGAA   ATGTT CA...AA ATGGT   CATGCCCGGC   GATAATGT GA 168 cuprinus Treponema CAGT GGTTAC   TGGC A TTGAG   ATGTT TA...AC ATGGT   GA A GCCGGGG   GATAACA CCA 169 pallidum Ureaplasma CTGT TGTTAC   AGGA A TTGAA   ATGTT TA...ATT TGGT   TATGCCAGGT   GAT G ACGT TG 170 urealyticum Wolinella CA ACCGTAAC   TGGCGTTGAG   ATGTT CC...AG ATGGT   TATGCCTGGT   GACAACGT TA 171 succinogenes Candida GTGT T AC CAC   TG A AGTC A AR  TCCG T TG...AGRAAT T   G GAAGA A AA T  CC AAA AT T CG 120 albicans Schizo- GTGT C AC TAC   CG A AGTC A AG  TCTG T TG...AG A A G A T   T GA G GA G TC C  CC TAA GT T TG saccharomyces pombe Human TG ACAGGCA T TG A G A TG TTC CACAAGA...AG A A GG A G C T TG CC AT G  CC C GGG G AGG Selected^(a)    ACIKKIAC   IGGIGTIGAR   ATGTT        ATGGT IATGCCIGGI   GAIAAYRT sequences^(a) Selected        SEQ ID NO:23                        SEQ ID NO:24^(b) universal primer   ACIKKIAC IGGIGTIGAR ATGTT        AYRTT ITCICCIGGC ATIACCAT sequences^(a):

[0168] Annex II: Strategy for the selection from tuf sequences of the amplification primers specific for the genus Enterococcus. SEQ ID NO 314                                348   401                                435 Bacillus CGCGAC ACTG   A A AAACCATT   CATGATG CCA GTTGA...CGCGG ACAA GTT AAA GT C GGTGACG   AAGTT GAAAT 148 subtilis Bacteroides CGCGA T GT TG   A T AAACC T TT   C T TGATG CCG GTAGA...ACTGG TGTTA T C C AT GT A GGTGA T G   AA A T CGAAAT 149 fragilis Burkholderia CGTGCAGT TG   AC GGCG C G TT   C C TGATG CCG GTGGA...CGCGG CATC GT GAAG GT C GG C GA A G   AA A T CGAAAT 152 cepacia Chlamydia AGAGAA A T TG   ACAA G CC T TT   C T T A ATG CCT ATTGA...CGTGG AATT GTT AAA GTT TCC GA TA AAGTT CAGTT 153 trachomatis Corynebacterium CGTGAG AC C G   ACAA G CCATT   C C T C ATG CCT ATCGA...CGTGG CTCCC T GAAG GT CAAC GA G G   A C GT CGAGAT 126 diphteriae Enterococcus CGTGA TACTG   ACAAACCATT   CATGATG CCA GTCGA...CGTGG ACAA GTTCGC   GTTGGTGACG   AAGTT GAAAT 131 avium Enterococcus CGTGA TACTG   ACAAACCATT   CATGATG CCA GTCGA...CGTGG TGAA GTTCGC   GTTGGTGACG   AAGTT GAAAT 132 faecalis Enterococcus CGTGAC A AC G   ACAAACCATT   CATGATG CCA GTTGA...CGTGG ACAA GTTCGC   GTTGGTGACG   AAGTT GAAGT 133 faecium Enterococcus CGTGA TACTG   ACAAACCATT   CATGATG CCA GTCGA...CGTGG ACAA GTTCGC   GTTGGTGA T G   AAGT AGAAAT 134 gallinarum Escherichia CGTGCG A T TG   ACAA G CC G TT   C C TG C TG CCG ATCGA...CGCGG TATCA T CAAA GTTGGTGA A G   AAGTT GAAAT 154 coli Gardnerella CACGA T CT TG   ACAA G CCATT   C T TGATG CCA ATCGA...CGTGG TAAGC T C C CA A T CAACAC C C C AGTT GAGAT 135 vaginalis Haemophilus CGTGCG A T TG   AC C AACC G TT   C C T TC T TCCA ATCGA...CGAGG TATTA T C CG T ACA GGTGA T G   AAGT AGAAAT 157 influenzae Helicobacter AGAGAC ACTG   A A AAA A C T TT   C T TGATG CCG GTTGA...AGAGG CGTG GT GAAA GT A GG C GA T G   AAGT GGAAAT 158 pylori Listeria CGTGA TACTG   ACAAACCATT   CATGATG CCA GTTGA...CGTGG ACAA GTT AAA GTTGGTGACG   AAGT AGAAGT 138 monocytogenes Micrococcus CGCGAC A AG G   ACAA G CC G TT   C C TGATG CCG ATCGA...CGCGG CACCC T GAAG A T CAACTC CG   A G GT CGAGAT 159 luteus Mycobacterium CGCGAG AC C G   ACAA G CC G TT   C C TGATG CCG GTCGA...CGCGG CGTGA T CCA C   GT GAAC GA G G   AAGTT GAGAT 160 tuberculosis Mycoplasma CGTGAAGTA G   A T AAACC T TT   C T T AT T AGCA ATTGA...AGAGG TGAAC T CAAA GT A GGT C A A G   AAGTT GAAAT 161 genitalium Neisseria CGTGCCGTG G   ACAAACCATT   C C TG C TG CCT ATCGA...CGAGG TATCA T C C A C   GTTGGTGACG   A GA TT GAAAT 162 gonorrhoeae Salmonella CGTGCG A T TG   ACAA G CC G TT   C C TG C TG CCG ATCGA...CGCGG TATCA T CAAA GT G GG C GA A G   AAGTT GAAAT 164 typhimurium Shewanella CGTGAC A TC G   A T AA G CC G TT   C C T AC TG CCA ATCGA...CGTGG TATT GT A CGC   GT A GG C GACG   AAGTT GAAAT 165 putida Staphylococcus CGTGA T T CTG   ACAAACCATT   CATGATG CCA GTTGA...CGTGG TCAAA T CAAA GTTGGTGA A G   AAGTT GAAAT 140 aureus Staphylococcus CGTGA T T CTG   ACAAACCATT   CATGATG CCA GTTGA...CGTGG TCAAA T CAAA GTTGGTGA A G   AAGTT GAAAT 141 epidermidis Staphylococcus CGTGA T T CTG   ACAAACCATT   CATGATG CCA GTTGA...CGTGG TCAAA T CAAA GT C GGTGA A G   AA A T CGARAT 142 saprophyticus Streptococcus CGTGA TACTG   ACAAACC T TT  AC T TC T TCCA GTTGA...CGTGG TACT GTTCG T GT CAAC GACG   AAGTT GAAAT 144 agalactiae Streptococcus CGTGAC ACTG   ACAAACCATT  GC T TC T TCCA GTCGA...CGTGG TATC GTT AAA GT CAAC GACG   AA A T CGAAAT 145 pneumoniae Streptococcus CGCGAC ACTG   ACAAACCATT  GC T TC T TCCA GTCGA...CGTGG TACT GTTCG T GT CAAC GACG   AA A T CGAAAT 167 pyogenes Ureaplasma CGTAG TACTG   ACAAACCATT   C T T AT T AGCA ATTGA...CGTGG TGTAT T AAAA GTT AA TGA T G   A G GTT GAAAT 167 urealyticum Selected       TACTG   ACAAACCATT   CATGATG                        GTTCGC   GTTGGTGACG   AAGTT sequences Selected           SEQ ID NO:13                                  SEQ ID NO:14^(a) genus-specific primer      TACTG ACAAACCATT CATGATG                      AACTTC GTCACCAACG CGAAC sequences: NOTE: The above primers also amplify tuf sequences from Abiotrophia species; this genus has recently been related to the Enterococcus genus by 16S rRNA analysis.

[0169] Annex III: Strategy for the selection from tuf sequences of the amplification primers specific for the genus Staphylococcus. SEQ ID NO 385                               420.....579                              611 Bacillus TGG CCGTTGT A GAACG C GG A C   AA G T T AAA GT CGG.....TTG CTAAA CC A GG   TACAATCAC T CCACACA GCA 148 subtilis Bacteroides AGGT CGT A T C GAA AC TGGT G TT ATC C A TGT AGG.....TTT GTAAA CC G GG   T CAG ATTA A A   CC T CAC TCTA 149 fragilis Burkholderia GGGT CGTGT C GA G CG C GG CA TCG T G AA GGT CGG.....TGG CGAAG CC G GG   TTC G ATCAC G CC G CACA CGC 152 cepacia Chlamydia TGGA CGT A TT   GA G CGTGG AA TTG T T AAA GT TTC.....TTT GCTTG CC AAA CA G T G TTA A A   CC T CATA CAC 153 trachomatis Corynebacterium CGG CCGTGTT   GA G CGTGG CT CCC T G AA GGT CAA.....TTG TTAAG CC A GG   C G CT TA CAC C CC T CACA CCG 126 diphteriae Enterococcus AGGA CGTGTT   GAACGTGGT G AA G T TCGCGT TGG.....TAG CTAAA CC A G C TACAATCAC T CCACACA CAA 132 faecalis Enterococcus AGGT CGTGTT   GAACGTGG A C   AA G T TCGCGT TGG.....TAG CTAAA CC A GG   TACAATCACA   CC T C R TA CAA 133 faecium Escherichia CGGT CGTGT A GAACG C GGT A TC ATCAAA GT TGG.....TGG CTAAG CC G GG   CAC C ATCA AG CC G CACA CCA 154 coli Gardnerella CGGT CGTGTT   GA G CGTGGT A A GC TC CC A AT CAA.....TGG CT GCTCC A GG   TTCT G T G AC T CCACACA CCA 135 vaginalis Haemophilus AGGT CGTGT A GAACG A GGT A TT ATC CGTAC AGG.....TAG CGAAA CC A GG   TTCAATCACA   CCACACA CGT 157 influenzae Helicobacter AGGTA G GA TT   GAA A G A GG CG TGG T G AAA GT AGG.....TAT GCAAA CC A GG   TTCTATCAC T CC G CACA AGA 158 pylori Listeria TGGA CGTGTT   GAACGTGG A C   AA G T T AAA GT TGG.....TAG CTAAA CC A GG   TTC G ATTAC T CCACACA CTA 138 monocytogenes Micrococcus CGGT CG C G CC GA G CG C GG CA CCC T G AA GAT CAA.....TGG TG G AG CC G GG   CTC C ATCAC C CC G CACA CCA 159 luteus Mycobacterium CGGA CGTGT G GA G CG C GG CG TG ATCAA CGT GAA.....TCA CCAAG CC C GG   CAC C A C CAC G CC G CACA CCG 160 tuberculosis Mycoplasma AGGAA G A GTT   GAA A G A GGT G AA C TCAAA GT AGG.....TAG CAAAA CC A GG   CTCTATTA A A   CC G CACA AGA 161 genitalium Neisseria CGG CCGTGT A GA G CG A GGT A TC ATC C A CGT TGG.....TGG CCAAA C GG GG   TACTATCAC T CC T CACA CCA 162 gonorrhoeae Salmonella CGGT CGTGT A GA G CG C GGT A TC ATCAAA GT GGG.....TGG CTAAG CC G GG   CAC C ATCA AG CC G CACA CCA 164 typhimurium Shewanella AGGT CGTGTT   GA G CGTGGT A TTG T ACGCGT AGG.....TAG CGAAG CC A GG TTCAATCA AC CCACACA CTA 165 putida Staphylococcus AGG CCGTGTT   GAACGTGGTC   AAATCAAA GT TGG.....TAG CT GCTCCTGG   TTCAATTACA   CCACATA CGT 140 aureus Staphylococcus AGG CCGTGTT   GAACGTGGTC   AAATCAAA GT WGG.....TAG CT GCTCCTGG   TTCTATTACA   CCACACA CAA 141 epidermidis Staphylococcus AGG CCGTGTT   GAACGTGGTC   AAATCAAA GT CGG.....TAG CT GCTCCTGG   TACTATCACA   CCACATA CAA 142 saprophyticus Staphylococcus AGG CCGTGTT   GAACGTGGTC   AAATCAAA GT CGG.....TAG CA GCTCCTGG   CTCTATTAC T CCACACA CAA 143 simulans Streptococcus AGGA CGT A T C GA CC GTGGT A CTG T TCGTGT CAA.....TGG CTAAA CC A GG TTCAATCA AC CCACACA CTA 144 agalactiae Steptococcus AGGA CGT A T C GA C CGTGGT A TCG T T AAA GT CAA.....TCG CTAAA CC A GG TTCAATCA AC CCACACA CTA 145 pneumoniae Ureaplasma TGGA CGTGTT   GAACGTGGT G T A T T A AAA GT TAA.....TTG TAAAA CC A GG  A TCAATTA A A   CC T CAC CGTA 170 urealyticum Selected      CCGTGTT   GAACGTGGTC   AAATCAAA                  GCTCCTGG   YWCWATYACA   CCACAYA sequences^(a) Selected            SEQ ID NO:17                                SEQ ID NO:18^(b) genus-specific primer     CCGTGTT GAACGTGGTC AAATCAAA                TRTGTGGT GTRATWGWRC CAGGAGC sequences^(a):

[0170] Annex IV: Strategy for the selection from tuf sequences of the amplification primers specific for the species Candida albicans. SEQ ID NO 58                                90   181                              213 Candida CGT CAAGAAG   GTTGGTTACA   ACCCAAAGA C TGT...CAA ATCCGGTAAA   GTTACTGGTA   AGACCT TGTT 120 albicans Candida CAT CAAGAAG   GT C GGTTACA   ACCCAAAGA C TGT...CAA GG C T GGT GTC GT C A AG GGTA   AGA Y CT TGTT 121 glabrata Candida CAT CAAGAAG   GTTGGTTACA   ACCCAAAGA C TGT...CAA GG C A GGT GTT GTTA AG GGTA   AGACCT TATT 122 krusei Candida CGT CAAGAAG   GTTGGTTACA   ACCC T AA AGC TGT...TAA A G C T GGTAA G GTTAC C GGTA   AGACCT TGTT 123 parapsilosis Candida CGT CAAGAAG   GTTGGTTACA   ACCC T AAG GC TGT...CAA GG C T GGTAA G GTTAC C GGTA   AGAC T T TGTT 124 tropicalis Schizo- CAT CAAGAAG   GT C GGTT T CA   ACCC C AAGA C CGT...CAA GG C T GGT GTC GT C A AG GGTA   AGAC TCTTTT saccharomyces pombe Human GGAG A TCCG G   G AGCTGCT CA  CCGAGTTTGG CTA...GTT A GG C CTG AA G TC T GTGCAG A   AG CTACTGGA 153 Chlamydia GGAGCT G CGC G AGCTGCT CA  G C AAGT A CGG CTT...CAA AT G....... .. TA T T CTGG AG CTGATGAA trachomatis Corynebacterium GGAG A TCCRT G AGCTGCTCG CTGAGC AG GA TTA...GAA GTGGACCC A G TCC A TCATCG A CCT C ATGCA 153 diphteriae Enterococcus GGAAGTTCGT G ACTTA T TAT CAGA A CGA TTT...... ...T G AAG AA  AAA A TCTTAG A ATTAATGGC 132 faecalis Escherichia GGAAGTTCGT G AACT T CTGT CT C AGT A CGA CTT...... ..GG G AAGCG AAA A TCCTGG A ACTGGCTGG 154 coli Flavobacterium CGAGGTTCGC G AA G AACTG A  CTAA A CGCGG TTT...... ..GG G T TAAA   G AA A T TG AA A   A CCTGATGGA 156 ferrugineum Gardnerella AGAGGTCCGT G ACCTCCTCG A AGA AAA CGG CTT...CAA G T GG G TAG A G ACCGTCAAGG A ACT C ATGAA 135 vaginalis Haemophilus GGAAGTTCGT G AACT T CTAT CT C A A T A TGA CTT...... ..GG G AAG AA AAA A TCCT T G AG TTAGCAAA 157 influenzae Listeria GGAA A TTCGT G A T CTA T TA A  CTG A A T A TGA ATT...... ..GG G AAGCT AAA A T TG ACG AG TTAATGGA 138 monocytogenes Micrococcus GGAA A TTCGT G AGTTGCTGG CTG C CC AG GA ATT...CAA G T GG G TCG A G TC T GTCACAC AG TTGATGGA 159 luteus Neisseria GGAA A TCCGC G ACCTGCTGT C C AGCT A CGA CTT...... ..A CG AAG AA  AAA A TCTTCG A ACTGGCTAC 162 gonorrhoeae Salmonella GGAAGTTCGC G AACTGCTGT CT C AGT A CGA CTT...... ..GG G AAGCG AAA A TCATCG A ACTGGCTGG 164 typhimurium Staphylococcus GGAAGTTCGT G ACTTA T TA A  GCGA A T A TGA CTT...... ... CG AAG AA  AAA A TCTTAG A ATTAATGGA 140 aureus Streptococcus GGAA A TCCGT G ACCTA T TGT CAGA A T A CGA CTT...... ... CG AAG A C A T CGT T ATGG A ATTGATGAA 145 pneumoniae Treponema AGAGGT G CGT G A TG CGCTTG CTGG A T A TGG GTT...GGA GGAT G CAGCT TG TA T TG AGG A ACTGCTTGC 169 Selected     CAAGAAG   GTTGGTTACA   ACCCAAAGA              ATCCGGTAAA   GTTACTGGTA   AGACCT sequences Selected            SEQ ID NO:11                           SEQ ID NO:12^(a) species-specific primer    CAAGAAG GTTGGTTACA ACCCAAAGA            AGGTCTTACC AGTAACTTTAC CGGAT sequences:

[0171] Annex V: Strategy for the selection from the recA gene of the amplification primers specific for the genus Streptococcus. SEQ ID NO 415                                449...540                                574 Bordetella CTC GA G AT CA C C G A C GCGC T   G G T GCGCTCG GGCTC...GGCCC GCC TGATGAG  C CAGGC GC TG   CG C AA GCTGA pertussis Burkholderia CTC GAAA TCA C C G A T GCGC T   G G T GCGCTCG GGCTC...GGCCC GCC TGATG TC G CAGGC GC TG   CG C AA GCTGA cepacia Campylobacter TTA GAAATTG  T AG A AA CTA T  AGCAAGAAGT GGCGC...AGCAA GAC T T ATG TC TCAAGC TC T A A G A AA ACTTA jejuni Chlamydia TTGAGT ATTG   CAG A G CTC TT  AGCGCGTTCT GGAGC...AGCTC GC ATGATG TC G CAGGC TC T A CG C AA ATTAA trachomatis Clostridium TTA GAAAT AA CAG A A GCT TT  AG TT AGATCA GGAGC...AGCTA GAT T A ATG TC A CAAGCC T T A AGA AA GTTAA perfringens Corynebacterium CTG GA G ATTG   CAG A TA TGC T  TG TT CGCTCT GGAGC...AGCGC GTT TGATGAG   TCAGGC GC TG   CGTAA GATGA pseudotuberculosis Enterobacter CTG GAAAT CT GT G A T GCGC T   GA CCCGTTCA GGCGC...AGCTC GT ATGATGAG  C CAGGC G ATG   CGTAA GCTTG agglomerans Enterococcus TTA GA G AGGT   C C G A T GC TT  AG TT TCAAGT GGTGC...AGCTC GAC T A ATG TC TCAAGC ACTA CGTAA ATTAT faecium Escherichia CTG GAAAT CT GT G A C GCCC T   G GCGCGTTCT GGCGC...GGCAC GT ATGATGAG  C CAGGC G ATG   CGTAA GCTGG coli Haemophilus GCGA A C A GAA G A AT A G AATT  TTAATGCATT ACCGC...GACCT GTGA G T T T A C G CAA AG C T TG  A G AC A TTAAA influenzae Helicobacter TTA GAAATT T T AG A AA CGA T  C A CCAGAAGC GGAGG...AGCAA GGC T T ATGAG  C CATGC GT T A A G A AA AATCA pylori Lactococcus CTTC AAATTG   C T G A AAAATT   GATT ACTTCT GGAGC...AGCAC GT ATGATG TC A CAAGCCATG   CGTAA ACTTG lactis Legionella CTG GAAATT A C T G A TA TGC T   G G T GCGTTCT GCAGC...GGCAA GAT TGATG TC G CAAGCC C TG   CGTAA ATTGA pneumophila Mycoplasma TTT G CTC TT A TC G A A TCATT A ATT A A AACA AACAA...TGCAA GA ATGATG TC AA AAG GTT+B,uns TG  CG C AA ACTGA genitalium Neisseria TTG GAAAT CT GC G A CA CGCT CG T CCGTTCG GGCGG...GGCGC GCC TGATGAG   TCAGGC TT TG   CG C AA ACTGA gonorrhoeae Proteus CTG GAAATT T GT G A T GC ATT  ATC T CGCTCT GGTGC...CGCAC GT ATGATGAG  C CAAGC T ATG   CGTAA ACTAG mirabilis Pseudomonas CTG GAAAT CA C C G A CA TGC T   G G T GCGCTCC AACGC...GGCAC GCC TGATG TC C CAGGC GC TG   CG C AA GATCA aeruginosa Serratia CTG GAAAT CT GT G A T GCGC T   GA CCCGCTCC GGCGC...GGCGC GC ATGATGAG  C CAGGC G ATG   CGTAA GCTGG marcescens Shigella CTG GAAAT CT GT G A C GCCC T   G GCGCGTTCT GGCGC...GGCAC GT ATGATGAG  C CAGGC G ATG CGTAA GCTGG flexneri Staphylococcus CTT GAAAT C G   C C G A A GC ATT  TG TT AGAAGT GGTGC...AGCTC GTT T A ATG TC A CAAGC GT T A CGTAA ACTTT aureus Streptococcus TTA GAAATTG CAGGAAAATT   GATTGACTCT GGGGC........ .......... .......... .......... 32 gordonii Streptococcus CTT GAAATTG   CAGGGAAATT   GATTGA TTCT GGCGC...AGCAC GC ATGATGAG   TCAAGC G ATG   CGTAA ATTAT 33 mutans Streptococcus CTT GA G ATTG   C G GGAAAATT   GATTGA CTCA GGTGC...GGCTC GT ATGATGAG  C CAGGCCATG   CGTAA ACTTG 34 pneumoniae Streptococcus CTT GAAATTG   CAGGTAAATT   GATTGA TTCT GGTGC...AGCAC GT ATGATGAG   TCAGGCCATG   CGTAA ATTAT 35 pyogenes Streptococcus CTC GAAATTG   CAGGTAA GCT GATTGA CTCT GGTGC...AGCGC GT ATGATGAG   TCAAGCCATG   CGTAA ACTTT 36 salivarius Vibrio CTG GAAATT T GT G A T GC A C T   G GC T CGCTCT GGTGC...AGCGC GT ATG T TG TC G CAAGC A ATG   CGTAA ACTGA cholerae Yersinia CTG GAAATT T GT G A T GC A C T   G GC T CGCTCT GGTGC...AGCGC GT ATG T TG TC G CAAGC A ATG   CGTAA ACTGA pestis Selected     GAAATTG   CAGGIAAATT   GATTGA                       ATGATGAG   TCAIGCCATG   CGTAA sequences^(a) Selected           SEQ ID NO:21                                   SEQ ID NO:22^(b) genus-specific primer    GAAATTG CAGGIAAATT GATTGA                     TTACGCAT GGCITGACTC ATCAT

[0172] Annex VI: Specific and ubiquitous primers for DNA amplification Originating DNA fragment SEQ ID Nucleotide SEQ ID NO Nucleotide sequence NO position Bacterial species: Enterococcus faecium  1 5′-TGC TTT AGC AAC AGC CTA TCA G  26^(a) 273-294  2^(b) 5′-TAA ACT TCT TCC GGC ACT TCG  26^(a) 468-488 Bacterial species: Listeria monocytogenes  3 5′-TGC GGC TAT AAA TGA AGA GGC  27^(a) 339-359  4^(b) 5′-ATC CGA TGA TGC TAT GGC TTT  27^(a) 448-468 Bacterial species: Neisseria meningitidis  5 5′-CCA GCG GTA TTG TTT GGT GGT  28^(a)  56-76  6^(b) 5′-CAG GCG GCC TTT AAT AAT TTC  28^(a) 212-232 Bacterial species: Staphylococcus saprophyticus  7 5′- AGA TCG AAT TCC ACA TGA AGG TTA TTA TGA  29^(c) 290-319  8^(b) 5′-TCG CTT CTC CCT CAA CAA TCA AAC TAT CCT  29^(c) 409-438 Bacterial species: Streptococcus agalactiae  9 5′-TTT CAC CAG CTG TAT TAG AAG TA  30^(a)  59-81 10^(b) b 5′-GTT CCC TGA ACA TTA TCT TTG AT  30^(a) 190-212 Fungal species: Candida albicans 11 5′-CAA GAA GGT TGG TTA CAA CCC AAA GA 120^(c)  61-86 12^(b) 5′-AGG TCT TAC CAG TAA CTT TAC CGG AT 120^(c) 184-209 ^(a) Sequences from databases. ^(b) These sequences are from the opposite DNA strand of the sequence of the   originating fragment given in the Sequence Listing. ^(c) Sequences determined by our group. Bacterial genus: Enterococcus 13 5′-TAC TGA CAA ACC ATT CAT GAT G 131-134^(a,b) 319-340^(c) 14^(d) 5′-AAC TTC GTC ACC AAC GCG AAC 131-134^(a,b) 410-430^(c) Bacterial genus: Neisseria 15 5′-CTG GCG CGG TAT GGT CGG TT  31^(e)  21-40^(f) 16^(d) 5′-GCC GAC GTT GGA AGT GGT AAA G  31^(e) 102-123^(f) Bacterial genus: Staphylococcus 17 5′-CCG TGT TGA ACG TGG TCA AAT CAA A 140-143^(a,b) 391-415^(g) 18^(d) 5′-TRT GTG GTG TRA TWG WRC CAG GAG C 140-143^(a,b) 584-608^(g) 19 5′-ACA ACG TGG WCA AGT WTT AGC WGC T 140-143^(a,b) 562-583 20^(d) 5′-ACC ATT TCW GTA CCT TCT GGT AAG T 140-143a,b 729-753^(g) Bacterial genus: Streptococcus 21 5′-GAA ATT GCA GGI AAA TTG ATT GA  32-3^(6e) 418-440^(h) 22^(d) 5′-TTA CGC ATG GCI TGA CTC ATC AT  32-36^(a) 547-569^(h) Universal primers 23 5′-ACI KKI ACI GGI GTI GAR ARG TT 118-146^(a,b) 493-515^(i) 147-171^(a,b) 24^(d) 5′-AYR TTI TCI CCI GGC ATI ACC AT 118-146^(a,b) 778-800^(i) 147-171^(a,e)

[0173] Annex VI: Specific and ubiquitous primers for DNA amplification Originating DNA fragment SEQ ID Nucleotide SEQ ID NO Nucleotide sequence NO position Antibiotic resistance gene: bla _(tan)  37 5′-CTA TGT GGC GCG GTA TTA TC — —  38 5′-CGC AGT GTT ATC ACT CAT GG — —  39 5′-CTG AAT GAA GCC ATA CCA AA — —  40 5′-ATC AGC AAT AAA CCA GCC AG — — Antibiotic resistance gene: bla _(ahv)  41 5′-TTA CCA TGA GCG ATA ACA GC — —  42 5′-CTC ATT CAG TTC CGT TTC CC — —  43 5′-CAG CTG CTG CAG TGG ATG GT — —  44 5′-CGC TCT GCT TTG TTA TTC GG — — Antibiotic resistance gene: bla _(rob)  45 5′-TAC GCC AAC ATC GTG GAA GT — —  46 5′-TTG AAT TTG GCT TCT TCG GT — —  47 5′-GGG ATA CAG AAA CGG GAC AT — —  48 5′-TAA ATC TTT TTC AGG CAG CG — — Antibiotic resistance gene: bla _(oxa)  49 5′-GAT GGT TTG AAG GGT TTA TTA TAA G 110^(a) 686-710  50^(b) 5′-AAT TTA GTG TGT TTA GAA TGG TGA T 110^(a) 802-826 Antibiotic resistance gene: blaZ  51 5′-ACT TCA ACA CCT GCT GCT TTC 111^(a) 511-531  52^(b) 5′-TGA CCA CTT TTA TCA GCA ACC 111^(a) 663-683 Antibiotic resistance gene: aadB  53 5′-GGC AAT AGT TGA AAT GCT CG — —  54 5′-CAG CTG TTA CAA CGG ACT GG — — Antibiotic resistance gene: aacCl  55 5′-TCT ATG ATC TCG CAG TCT CC — —  56 5′-ATC GTC ACC GTA ATC TGC TT — — Antibiotic resistance gene: aacC2  57 5′-CAT TCT CGA TTG CTT TGC TA — —  58 5′-CCG AAA TGC TTC TCA AGA TA — — Antibiotic resistance gene: aacC3  59 5′-CTG GAT TAT GGC TAC GGA GT — —  60 5′-AGC AGT GTG ATG GTA TCC AG — — Antibiotic resistance gene: aac6′-IIa  61 5′-GAC TCT TGA TGA AGT GCT GG 112^(a) 123-142  62^(b) 5′-CTG GTC TAT TCC TCG CAC TC 112^(a) 284-303  63 5′-TAT GAG AAG GCA GGA TTC GT 112^(a) 445-464  64^(b) 5′-GCT TTC TCT CGA AGG CTT GT 112^(a) 522-541 Antibiotic resistance gene: aacA4  65 5′-GAG TTG CTG TTC AAT GAT CC — —  66 5′-GTG TTT GAA CCA TGT ACA CG — — Antibiotic resistance gene: aad(6′) 173 5′-TCT TTA GCA GAA CAG GAT GAA — — 174 5′-GAA TAA TTC ATA TCC TCC G — — Antibiotic resistance gene: vanA  67 5′-TGT AGA GGT CTA GCC CGT GT — —  68 5′-ACG GGG ATA ACG ACT GTA TG — —  69 5′-ATA AAG ATG ATA GGC CGG TG — —  70 5′-TGC TGT CAT ATT GTC TTG CC — — Antibiotic resistance gene: vanB  71 5′-ATT ATC TTC GGC GGT TGC TC 116^(a) 22-41  72^(b) 5′-GAC TAT CGG CTT CCC ATT CC 116^(a) 171-190  73 5′-CGA TAG AAG CAG CAG GAC AA 116^(a) 575-594  74^(b) 5′-CTG ATG GAT GCG GAA GAT AC 116^(a) 713-732 Antibiotic resistance gene: vanC  75 5′-GCC TTA TGT ATG AAC AAA TGG 117^(a) 373-393  76^(b) 5′-GTG ACT TTW GTG ATC CCT TTT GA 117^(a) 541-563 Antibiotic resistance gene: msrA  77 5′-TCC AAT CAT TGC ACA AAA TC — —  78 5′-AAT TCC CTC TAT TTG GTG GT — —  79 5′-TCC CAA GCC AGT AAA GCT AA — —  80 5′-TGG TTT TTC AAC TTC TTC CA — — Antibiotic resistance gene: satA  81 5′-TCA TAG AAT GGA TGG CTC AA — —  82 5′-AGC TAC TAT TGC ACC ATC CC — — Antibiotic resistance gene: aac(6′)-aph(2″)  83 5′-CAA TAA GGG CAT ACC AAA AAT C — —  84 5′-CCT TAA CAT TTG TGG CAT TAT C — —  85 5′-TTG GGA AGA TGA AGT TTT TAG A — —  86 5′-CCT TTA CTC CAA TAA TTT GGC T — — Antibiotic resistance gene: vat  87 5′-TTT CAT CTA TTC AGO ATG GG — —  88 5′-GGA GCA ACA TTC TTT GTG AC — — Antibiotic resistance gene: vga  89 5′-TGT GCC TGA AGA AGG TAT TG — —  90 5′-CGT GTT ACT TCA CCA CCA CT — — Antibiotic resistance gene: ermA  91 5′-TAT CTT ATC GTT GAG AAG GGA TT 113^(a) 370-392  92^(b) 5′-CTA CAC TTG GCT TAG GAT GAA A 113^(a) 487-508 Antibiotic resistance gene: ermB  93 5′-CTA TCT GAT TGT TGA AGA AGG ATT 114^(a) 366-389  94^(b) 5′-GTT TAC TCT TGG TTT AGG ATG AAA 114^(a) 484-507 Antibiotic resistance gene: ermC  95 5′-CTT GTT GAT CAC GAT AAT TTC C 115^(a) 214-235  96^(b) 5′-ATC TTT TAG CAA ACC CGT ATT C 115^(a) 382-403 Antibiotic resistance gene: mecA  97 5′-AAC AGG TGA ATT ATT AGC ACT TGT AAG — —  98 5′-ATT GCT GTT AAT ATT TTT TGA GTT GAA — — Antibiotic resistance gene: int  99 5′-GTG ATC GAA ATC CAG ATC C — — 100 5′-ATC CTC GGT TTT CTG GAA G — — 101 5′-CTG GTC ATA CAT GTG ATG G — — 102 5′-GAT GTT ACC CGA GAG CTT G — — Antibiotic resistance gene: aul 103 5′-TTA AGC GTG CAT AAT AAG CC — — 104 5′-TTG CGA TTA CTT CGC CAA CT — — 105 5′-TTT ACT AAG CTT GCC CCT TC — — 106 5′-AAA AGG CAG CAA TTA TGA GC — —

[0174]

1 174 1 22 DNA Enterococcus faecium 1 tgctttagca acagcctatc ag 22 2 21 DNA Enterococcus faecium 2 taaacttctt ccggcacttc g 21 3 21 DNA Listeria monocytogenes 3 tgcggctata aatgaagagg c 21 4 21 DNA Listeria monocytogenes 4 atccgatgat gctatggctt t 21 5 21 DNA Neisseria meningitidis 5 ccagcggtat tgtttggtgg t 21 6 21 DNA Neisseria meningitidis 6 caggcggcct ttaataattt c 21 7 30 DNA Staphylococcus saprophyticus 7 agatcgaatt ccacatgaag gttattatga 30 8 30 DNA Staphylococcus saprophyticus 8 tcgcttctcc ctcaacaatc aaactatcct 30 9 23 DNA Streptococcus agalactiae 9 tttcaccagc tgtattagaa gta 23 10 23 DNA Streptococcus agalactiae 10 gttccctgaa cattatcttt gat 23 11 26 DNA Candida albicans 11 caagaaggtt ggttacaacc caaaga 26 12 26 DNA Candida albicans 12 aggtcttacc agtaacttta ccggat 26 13 22 DNA Enterococcus sp. 13 tactgacaaa ccattcatga tg 22 14 21 DNA Enterococcus sp. 14 aacttcgtca ccaacgcgaa c 21 15 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 15 ctggcgcggt atggtcggtt 20 16 22 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 16 gccgacgttg gaagtggtaa ag 22 17 25 DNA Staphylococcus sp. 17 ccgtgttgaa cgtggtcaaa tcaaa 25 18 25 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 18 trtgtggtgt ratwgwrcca ggagc 25 19 25 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 19 acaacgtggw caagtwttag cwgct 25 20 25 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 20 accatttcwg taccttctgg taagt 25 21 23 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 21 gaaattgcag gnaaattgat tga 23 22 23 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 22 ttacgcatgg cntgactcat cat 23 23 23 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 23 acnkknacng gngtngarat gtt 23 24 23 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 24 ayrttntcnc cnggcatnac cat 23 25 10 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 25 tcgcttctcc 10 26 600 DNA Enterococcus faecium 26 ttcttagaga cattgaatat gccttatgtc ggcgcaggcg tattgaccag tgcatgtgcc 60 atggataaaa tcatgaccaa gtatatttta caagctgctg gtgtgccgca agttccttat 120 gtaccagtac ttaagaatca atggaaagaa aatcctaaaa aagtatttga tcaatgtgaa 180 ggttctttgc tttatccgat gtttgtcaaa cctgcgaata tgggttctag tgtcggcatt 240 acaaaggcag aaaaccgaga agagctgcaa aatgctttag caacagccta tcagtatgat 300 tctcgagcaa tcgttgaaca aggaattgaa gcgcgcgaaa tcgaagttgc tgtattagga 360 aatgaagatg ttcggacgac tttgcctggc gaagtcgtaa aagacgtagc attctatgat 420 tatgaagcca aatatatcaa taataaaatc gaaatgcaga ttccagccga agtgccggaa 480 gaagtttatc aaaaagcgca agagtacgcg aagttagctt acacgatgtt aggtggaagc 540 ggattgagcc ggtgcgattt ctttttgaca aataaaaatg aattattcct gaatgaatta 600 27 1920 DNA Listeria monocytogenes 27 gtgggattaa acagatttat gcgtgcgatg atggtggttt tcattactgc caattgcatt 60 acgattaacc ccgacataat atttgcagcg acagatagcg aagattctag tctaaacaca 120 gatgaatggg aagaagaaaa aacagaagag caaccaagcg aggtaaatac gggaccaaga 180 tacgaaactg cacgtgaagt aagttcacgt gatattaaag aactagaaaa atcgaataaa 240 gtgagaaata cgaacaaagc agacctaata gcaatgttga aagaaaaagc agaaaaaggt 300 ccaaatatca ataataacaa cagtgaacaa actgagaatg cggctataaa tgaagaggct 360 tcaggagccg accgaccagc tatacaagtg gagcgtcgtc atccaggatt gccatcggat 420 agcgcagcgg aaattaaaaa aagaaggaaa gccatagcat catcggatag tgagcttgaa 480 agccttactt atccggataa accaacaaaa gtaaataaga aaaaagtggc gaaagagtca 540 gttgcggatg cttctgaaag tgacttagat tctagcatgc agtcagcaga tgagtcttca 600 ccacaacctt taaaagcaaa ccaacaacca tttttcccta aagtatttaa aaaaataaaa 660 gatgcgggga aatgggtacg tgataaaatc gacgaaaatc ctgaagtaaa gaaagcgatt 720 gttgataaaa gtgcagggtt aattgaccaa ttattaacca aaaagaaaag tgaagaggta 780 aatgcttcgg acttcccgcc accacctacg gatgaagagt taagacttgc tttgccagag 840 acaccaatgc ttcttggttt taatgctcct gctacatcag aaccgagctc attcgaattt 900 ccaccaccac ctacggatga agagttaaga cttgctttgc cagagacgcc aatgcttctt 960 ggttttaatg ctcctgctac atcggaaccg agctcgttcg aatttccacc gcctccaaca 1020 gaagatgaac tagaaatcat ccgggaaaca gcatcctcgc tagattctag ttttacaaga 1080 ggggatttag ctagtttgag aaatgctatt aatcgccata gtcaaaattt ctctgatttc 1140 ccaccaatcc caacagaaga agagttgaac gggagaggcg gtagaccaac atctgaagaa 1200 tttagttcgc tgaatagtgg tgattttaca gatgacgaaa acagcgagac aacagaagaa 1260 gaaattgatc gcctagctga tttaagagat agaggaacag gaaaacactc aagaaatgcg 1320 ggttttttac cattaaatcc gtttgctagc agcccggttc cttcgttaag tccaaaggta 1380 tcgaaaataa gcgaccgggc tctgataagt gacataacta aaaaaacgcc atttaagaat 1440 ccatcacagc cattaaatgt gtttaataaa aaaactacaa cgaaaacagt gactaaaaaa 1500 ccaacccctg taaagaccgc accaaagcta gcagaacttc ctgccacaaa accacaagaa 1560 accgtactta gggaaaataa aacacccttt atagaaaaac aagcagaaac aaacaagcag 1620 tcaattaata tgccgagcct accagtaatc caaaaagaag ctacagagag cgataaagag 1680 gaaatgaaac cacaaaccga ggaaaaaatg gtagaggaaa gcgaatcagc taataacgca 1740 aacggaaaaa atcgttctgc tggcattgaa gaaggaaaac taattgctaa aagtgcagaa 1800 gacgaaaaag cgaaggaaga accagggaac catacgacgt taattcttgc aatgttagct 1860 attggcgtgt tctctttagg ggcgtttatc aaaattattc aattaagaaa aaataattaa 1920 28 415 DNA Neisseria meningitidis 28 taccggtacg ctaaatattg gtgatgtatt ggatattatg atttgggaag cgccgccagc 60 ggtattgttt ggtggtggcc tttcttcgat gggctcgggt agtgcgcaac aaaccaagtt 120 gccggagcaa ctggtgacgg cacgtggtac ggtttctgtg ccgtttgttg gcgatatttc 180 ggtggtcggt aaaacgcctg gtcaggttca ggaaattatt aaaggccgcc tgaaaaaaat 240 ggccaatcag ccgcaagtga tggtgcgctt ggtgcagaat aatgcggcaa atgtatcggt 300 gattcgcgca ggcaatagtg tgcgtatgcc gttgacggca gccggtgagc gtgtgttgga 360 tgcggtggct gcggtaggtg gttcaacggc aaatgtgcag gatacgaatg tgcag 415 29 438 DNA Staphylococcus saprophyticus 29 tcgcttctcc agaagaaatt ttagaaacat atctagaaaa tcccaaatta gataaaccgt 60 ttatattatg tgaatacgca catgcaatgg gaaattcacc aggagatctt aatgcatatc 120 aaacattaat tgaaaaatat gatagtttta ttggcggttt tgtttgggaa tggtgtgatc 180 atagcattca ggttgggata aaggaaggta aaccaatttt tagatatggt ggagattttg 240 gtgaggcctt acatgacggt aatttttgtg ttgatggtat tgtttcgcca gatcgaattc 300 cacatgaagg ttattatgag tttaaacatg aacatagacc tttgagattg gttaacgaag 360 aggattatcg gtttacattg aagaatcaat ttgattttac aaatgcggag gatagtttga 420 ttgttgaggg agaagcga 438 30 768 DNA Streptococcus agalactiae 30 atgaacgtta cacatatgat gtatctatct ggaactctag tggctggtgc attgttattt 60 tcaccagctg tattagaagt acatgctgat caagtgacaa ctccacaagt ggtaaatcat 120 gtaaatagta ataatcaagc ccagcaaatg gctcaaaagc ttgatcaaga tagcattcag 180 ttgagaaata tcaaagataa tgttcaggga acagattatg aaaaaccggt taatgaggct 240 attactagcg tggaaaaatt aaagacttca ttgcgtgcca accctgagac agtttatgat 300 ttgaattcta ttggtagtcg tgtagaagcc ttaacagatg tgattgaagc aatcactttt 360 tcaactcaac atttaacaaa taaggttagt caagcaaata ttgatatggg atttgggata 420 actaagctag ttattcgcat tttagatcca tttgcttcag ttgattcaat taaagctcaa 480 gttaacgatg taaaggcatt agaacaaaaa gttttaactt atcctgattt aaaaccaact 540 gatagagcta ccatctatac aaaatcaaaa cttgataagg aaatctggaa tacacgcttt 600 actagagata aaaaagtact taacgtcaaa gaatttaaag tttacaatac tttaaataaa 660 gcaatcacac atgctgttgg agttcagttg aatccaaatg ttacggtaca acaagttgat 720 caagagattg taacattaca agcagcactt caaacagcat taaaataa 768 31 421 DNA Neisseria meningitidis 31 atgaaagtag gtttcgtcgg ctggcgcggt atggtcggtt cggttttgat gcagcgtatg 60 aaagaagaaa acgacttcgc ccacattccc gaagcgtttt tctttaccac ttccaacgtc 120 ggcggcgcac gccctgattt cggtcaggcg gctaaaacat tattggacgc gaacaacgtt 180 gccgagctgg caaaaatgga catcatcgtt acctgccaag gcggcgacta caccaaatcc 240 gtcttccaag ccctgcgcga cagcggctgg aacggctact ggattgacgc ggcatcctcg 300 ctgcgtatga aagacgacgc gattatcgtc ctcgaccccg tcaaccgcaa cgtcatcgac 360 aacggcctca aaaacggcgt gaaaaactac atcggcggca actgtaccgt ttccctgatg 420 c 421 32 213 DNA Streptococcus gordonii 32 ttcatagacg ctgagcacgc tttggatcca tcttacgcgg ctgctctagg tgtaaatatt 60 gatgagctgt tgctatctca accagattct ggtgagcaag gtttagaaat tgcaggaaaa 120 ttgattgact ctggggcagt tgatttagtt gtcatcgact ctgttgcagc tcttgtacca 180 cgtgcggaaa tcgatggaga tatcggtgat agc 213 33 692 DNA Streptococcus mutans 33 gggccggaat cttctggtaa gacaactgtc gctcttcatg ctgctgctca ggcgcaaaaa 60 gatggcggta ttgccgcttt cattgatgca gaacatgccc ttgatccagc ctatgctgct 120 gctcttggcg ttaatattga tgagcttttg ctttcacaac cagattcagg agaacagggt 180 cttgaaattg cagggaaatt gattgattct ggcgctgttg atttagttgt tgttgactca 240 gtggcagctt tagtaccacg tgcggagatt gacggagata ttggtaatag tcatgttggc 300 ttacaagcac gcatgatgag tcaagcgatg cgtaaattat cagcttcaat caataaaaca 360 aaaaccattg ctatttttat taatcaattg cgggaaaaag ttggtattat gtttggtaat 420 ccagaaacaa cccctggcgg gcgtgccttg aagttttatt cttctgtgcg tcttgatgtc 480 cgcggcaata ctcaaattaa aggaaccggg gaacaaaaag acagcaatat tggtaaagag 540 accaaaatta aagttgttaa aaataaagtt gctccaccat ttaaggaagc ttttgtagaa 600 attatatatg gtgaaggcat ttctcgtaca ggtgaattag ttaagattgc cagtgatttg 660 ggaattatcc aaaaagctgg agcttggtac tc 692 34 1204 DNA Streptococcus pneumoniae 34 atggcgaaaa aaccaaaaaa attagaagaa atttcaaaaa aatttggggc agaacgtgaa 60 aaggccttga atgacgctct taaattgatt gagaaagact ttggtaaagg atcaatcatg 120 cgtttgggtg aacgtgcgga gcaaaaggtg caagtgatga gctcaggttc tttagctctt 180 gacattgccc ttggctcagg tggttatcct aagggacgta tcatcgaaat ctatggccca 240 gagtcatctg gtaagacaac ggttgccctt catgcagttg cacaagcgca aaaagaaggt 300 gggattgctg cctttatcga tgcggaacat gcccttgatc cagcttatgc tgcggccctt 360 ggtgtcaata ttgacgaatt gctcttgtct caaccagact caggagagca aggtcttgag 420 attgcgggaa aattgattga ctcaggtgca gttgatcttg tcgtagtcga ctcagttgct 480 gcccttgttc ctcgtgcgga aattgatgga gatatcggag atagccatgt tggtttgcag 540 gctcgtatga tgagccaggc catgcgtaaa cttggcgcct ctatcaataa aaccaaaaca 600 attgccattt ttatcaacca attgcgtgaa aaagttggag tgatgtttgg aaatccagaa 660 acaacaccgg gcggacgtgc tttgaaattc tatgcttcag tccgcttgga tgttcgtggt 720 aatacacaaa ttaagggaac tggtgatcaa aaagaaacca atgtcggtaa agaaactaag 780 attaaggttg taaaaaataa ggtagctcca ccgtttaagg aagccgtagt tgaaattatg 840 tacggagaag gaatttctaa gactggtgag cttttgaaga ttgcaagcga tttggatatt 900 atcaaaaaag caggggcttg gtattcttac aaagatgaaa aaattgggca aggttctgag 960 aatgctaaga aatacttggc agagcaccca gaaatctttg atgaaattga taagcaagtc 1020 cgttctaaat ttggcttgat tgatggagaa gaagtttcag aacaagatac tgaaaacaaa 1080 aaagatgagc caaagaaaga agaagcagtg aatgaagaag ttccgcttga cttaggcgat 1140 gaacttgaaa tcgaaattga agaataagct gttaaagcag tggagaaatc cgctactttt 1200 tcga 1204 35 981 DNA Streptococcus pyogenes 35 atgcgttcag gaagtctagc tcttgatatt gcttggatag ctggtggtta tcctaaagga 60 cgtatcatcg aaatctatgg tccagagtct tccggtaaaa cgactgtggc tttacatgct 120 gtagcacaag ctcaaaaaga aggtggaatc gcagccttta tcgatgccga gcatgcgctt 180 gatccagctt atgctgctgc gcttggggtt aatattgatg aacttctctt gtctcaacca 240 gattctggag aacaaggact tgaaattgca ggtaaattga ttgattctgg tgcggttgac 300 ctggttgttg tcgattcagt agcagcttta gtgccacgtg ctgaaattga tggtgatatt 360 ggcgatagcc atgtcggatt gcaagcacgt atgatgagtc aggccatgcg taaattatca 420 gcttctatta ataaaacaaa aactatcgca atctttatca accaattgcg tgaaaaagtt 480 ggtgtgatgt ttggaaatcc tgaaacaaca ccaggtggtc gagctttgaa attctatgct 540 tctgttcggc tggatgtgcg tggaaacaac caaattaaag gaactggtga ccaaaagata 600 gccagcattg gtaaggagac caaaatcaag gttgttaaaa acaaggtcgc tccgccattt 660 aaggtagcag aagttgaaat catgtatggg gaaggtattt ctcgtacagg ggagcttgtg 720 aaaattgctt ctgatttgga cattatccaa aaagcaggtg cttggttctc ttataatggt 780 gagaagattg gccaaggttc tgaaaatgct aagcgttatt tggccgatca tccacaattg 840 tttgatgaaa tcgaccgtaa agtacgtgtt aaatttggtt tgcttgaaga aagcgaagaa 900 gaatctgcta tggcagtagc atcagaagaa accgatgatc ttgctttaga tttagataat 960 ggtattgaaa ttgaagatta a 981 36 312 DNA Streptococcus salivarius 36 gcgtatgcac gagctctagg tgttaatatc gatgagcttc ttttgtcgca gcctgattct 60 ggtgagcaag gtctcgaaat tgcaggtaag ctgattgact ctggtgcagt ggatttagtt 120 gttgttgact cagttgcggc cttcgtacca cgtgcagaaa ttgatggaga tagtggtgac 180 agtcatgtag gacttcaagc gcgtatgatg agtcaagcca tgcgtaaact ttctgcatct 240 attaataaaa caaaaacgat tgctatcttt attaaccagt tgcgtgaaaa agttggtatc 300 atgtttggta ac 312 37 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 37 ctatgtggcg cggtattatc 20 38 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 38 cgcagtgtta tcactcatgg 20 39 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 39 ctgaatgaag ccataccaaa 20 40 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 40 atcagcaata aaccagccag 20 41 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 41 ttaccatgag cgataacagc 20 42 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 42 ctcattcagt tccgtttccc 20 43 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 43 cagctgctgc agtggatggt 20 44 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 44 cgctctgctt tgttattcgg 20 45 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 45 tacgccaaca tcgtggaaag 20 46 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 46 ttgaatttgg cttcttcggt 20 47 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 47 gggatacaga aacgggacat 20 48 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 48 taaatctttt tcaggcagcg 20 49 25 DNA Escherichia coli 49 gatggtttga agggtttatt ataag 25 50 25 DNA Escherichia coli 50 aatttagtgt gtttagaatg gtgat 25 51 21 DNA Enterococcus faecalis 51 acttcaacac ctgctgcttt c 21 52 21 DNA Enterococcus faecalis 52 tgaccacttt tatcagcaac c 21 53 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 53 ggcaatagtt gaaatgctcg 20 54 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 54 cagctgttac aacggactgg 20 55 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 55 tctatgatct cgcagtctcc 20 56 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 56 atcgtcaccg taatctgctt 20 57 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 57 cattctcgat tgctttgcta 20 58 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 58 ccgaaatgct tctcaagata 20 59 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 59 ctggattatg gctacggagt 20 60 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 60 agcagtgtga tggtatccag 20 61 20 DNA Pseudomonas aeruginosa 61 62 20 DNA Pseudomonas aeruginosa 62 ctggtctatt cctcgcactc 20 63 20 DNA Pseudomonas aeruginosa 63 tatgagaagg caggattcgt 20 64 20 DNA Pseudomonas aeruginosa 64 gctttctctc gaaggcttgt 20 65 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 65 gagttgctgt tcaatgatcc 20 66 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 66 gtgtttgaac catgtacacg 20 67 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 67 tgtagaggtc tagcccgtgt 20 68 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 68 acggggataa cgactgtatg 20 69 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 69 ataaagatga taggccggtg 20 70 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 70 tgctgtcata ttgtcttgcc 20 71 20 DNA Enterococcus faecalis 71 72 20 DNA Enterococcus faecalis 72 gactatcggc ttcccattcc 20 73 20 DNA Enterococcus faecalis 73 cgatagaagc agcaggacaa 20 74 20 DNA Enterococcus faecalis 74 ctgatggatg cggaagatac 20 75 21 DNA Enterococcus gallinarum 75 gccttatgta tgaacaaatg g 21 76 23 DNA Enterococcus gallinarum 76 gtgactttwg tgatcccttt tga 23 77 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 77 tccaatcatt gcacaaaatc 20 78 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 78 aattccctct atttggtggt 20 79 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 79 tcccaagcca gtaaagctaa 20 80 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 80 tggtttttca acttcttcca 20 81 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 81 tcatagaatg gatggctcaa 20 82 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 82 agctactatt gcaccatccc 20 83 22 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 83 caataagggc ataccaaaaa tc 22 84 22 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 84 ccttaacatt tgtggcatta tc 22 85 22 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 85 ttgggaagat gaagttttta ga 22 86 22 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 86 cctttactcc aataatttgg ct 22 87 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 87 tttcatctat tcaggatggg 20 88 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 88 ggagcaacat tctttgtgac 20 89 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 89 tgtgcctgaa gaaggtattg 20 90 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 90 cgtgttactt caccaccact 20 91 23 DNA Staphylococcus aureus 91 tatcttatcg ttgagaaggg att 23 92 22 DNA Staphylococcus aureus 92 ctacacttgg cttaggatga aa 22 93 24 DNA Escherichia coli 93 ctatctgatt gttgaagaag gatt 24 94 24 DNA Escherichia coli 94 gtttactctt ggtttaggat gaaa 24 95 22 DNA Staphylococcus aureus 95 cttgttgatc acgataattt cc 22 96 22 DNA Staphylococcus aureus 96 atcttttagc aaacccgtat tc 22 97 27 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 97 aacaggtgaa ttattagcac ttgtaag 27 98 27 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 98 attgctgtta atattttttg agttgaa 27 99 19 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 99 gtgatcgaaa tccagatcc 19 100 19 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 100 atcctcggtt ttctggaag 19 101 19 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 101 ctggtcatac atgtgatgg 19 102 19 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 102 gatgttaccc gagagcttg 19 103 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 103 ttaagcgtgc ataataagcc 20 104 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 104 ttgcgattac ttcgccaact 20 105 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 105 tttactaagc ttgccccttc 20 106 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 106 aaaaggcagc aattatgagc 20 107 29 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 107 aayatgatna cnggngcngc ncaratgga 29 108 23 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 108 ccnacngtnc knccrccytc rcg 23 109 29 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 109 carytnathg tngcngtnaa yaaratgga 29 110 831 DNA Escherichia coli 110 atgaaaaaca caatacatat caacttcgct atttttttaa taattgcaaa tattatctac 60 agcagcgcca gtgcatcaac agatatctct actgttgcat ctccattatt tgaaggaact 120 gaaggttgtt ttttacttta cgatgcatcc acaaacgctg aaattgctca attcaataaa 180 gcaaagtgtg caacgcaaat ggcaccagat tcaactttca agatcgcatt atcacttatg 240 gcatttgatg cggaaataat agatcagaaa accatattca aatgggataa aacccccaaa 300 ggaatggaga tctggaacag caatcataca ccaaagacgt ggatgcaatt ttctgttgtt 360 tgggtttcgc aagaaataac ccaaaaaatt agattaaata aaatcaagaa ttatctcaaa 420 gattttgatt atggaaatca agacttctct ggagataaag aaagaaacaa cggattaaca 480 gaagcatggc tcgaaagtag cttaaaaatt tcaccagaag aacaaattca attcctgcgt 540 aaaattatta atcacaatct cccagttaaa aactcagcca tagaaaacac catagagaac 600 atgtatctac aagatctgga taatagtaca aaactgtatg ggaaaactgg tgcaggattc 660 acagcaaata gaaccttaca aaacggatgg tttgaagggt ttattataag caaatcagga 720 cataaatatg tttttgtgtc cgcacttaca ggaaacttgg ggtcgaattt aacatcaagc 780 ataaaagcca agaaaaatgc gatcaccatt ctaaacacac taaatttata a 831 111 846 DNA Enterococcus faecalis 111 ttgaaaaagt taatattttt aattgtaatt gctttagttt taagtgcatg taattcaaac 60 agttcacatg ccaaagagtt aaatgattta gaaaaaaaat ataatgctca tattggtgtt 120 tatgctttag atactaaaag tggtaaggaa gtaaaattta attcagataa gagatttgcc 180 tatgcttcaa cttcaaaagc gataaatagt gctattttgt tagaacaagt accttataat 240 aagttaaata aaaaagtaca tattaacaaa gatgatatag ttgcttattc tcctatttta 300 gaaaaatatg taggaaaaga tatcacttta aaagcactta ttgaggcttc aatgacatat 360 agtgataata cagcaaacaa taaaattata aaagaaatcg gtggaatcaa aaaagttaaa 420 caacgtctaa aagaactagg agataaagta acaaatccag ttagatatga gatagaatta 480 aattactatt caccaaagag caaaaaagat acttcaacac ctgctgcttt cggtaagact 540 ttaaataaac ttatcgcaaa tggaaaatta agcaaagaaa acaaaaaatt cttacttgat 600 ttaatgttaa ataataaaag cggagatact ttaattaaag acggtgttcc aaaagactat 660 aaggttgctg ataaaagtgg tcaagcaata acatatgctt ctagaaatga tgttgctttt 720 gtttatccta agggccaatc tgaacctatt gttttagtca tttttacgaa taaagacaat 780 aaaagtgata agccaaatga taagttgata agtgaaaccg ccaagagtgt aatgaaggaa 840 ttttaa 846 112 555 DNA Pseudomonas aeruginosa 112 atgtccgcga gcaccccccc cataactctt cgcctcatga ccgagcgcga cctgccgatg 60 ctccatgact ggctcaaccg gccgcacatc gttgagtggt ggggtggcga cgaagagcga 120 ccgactcttg atgaagtgct ggaacactac ctgcccagag cgatggcgga agagtccgta 180 acaccgtaca tcgcaatgct gggcgaggaa ccgatcggct atgctcagtc gtacgtcgcg 240 ctcggaagcg gtgatggctg gtgggaagat gaaactgatc caggagtgcg aggaatagac 300 cagtctctgg ctgacccgac acagttgaac aaaggcctag gaacaaggct tgtccgcgct 360 ctcgttgaac tactgttctc ggaccccacc gtgacgaaga ttcagaccga cccgactccg 420 aacaaccatc gagccatacg ctgctatgag aaggcaggat tcgtgcggga gaagatcatc 480 accacgcctg acgggccggc ggtttacatg gttcaaacac gacaagcctt cgagagaaag 540 cgcggtgttg cctaa 555 113 732 DNA Staphylococcus aureus 113 atgaaccaga aaaaccctaa agacacgcaa aattttatta cttctaaaaa gcatgtaaaa 60 gaaatattga atcacacgaa tatcagtaaa caagacaacg taatagaaat cggatcagga 120 aaaggacatt ttaccaaaga gctagtcaaa atgagtcgat cagttactgc tatagaaatt 180 gatggaggct tatgtcaagt gactaaagaa gcggtaaacc cctctgagaa tataaaagtg 240 attcaaacgg atattctaaa attttccttc ccaaaacata taaactataa gatatatggt 300 aatattcctt ataacatcag tacggatatt gtcaaaagaa ttacctttga aagtcaggct 360 aaatatagct atcttatcgt tgagaaggga tttgcgaaaa gattgcaaaa tctgcaacga 420 gctttgggtt tactattaat ggtggagatg gatataaaaa tgctcaaaaa agtaccacca 480 ctatattttc atcctaagcc aagtgtagac tctgtattga ttgttcttga acgacatcaa 540 ccattgattt caaagaagga ctacaaaaag tatcgatctt ttgtttataa gtgggtaaac 600 cgtgaatatc gtgttctttt cactaaaaac caattccgac aggctttgaa gcatgcaaat 660 gtcactaata ttaataaact atcgaaggaa caatttcttt ctattttcaa tagttacaaa 720 ttgtttcact aa 732 114 738 DNA Escherichia coli 114 atgaacaaaa atataaaata ttctcaaaac tttttaacga gtgaaaaagt actcaaccaa 60 ataataaaac aattgaattt aaaagaaacc gataccgttt acgaaattgg aacaggtaaa 120 gggcatttaa cgacgaaact ggctaaaata agtaaacagg taacgtctat tgaattagac 180 agtcatctat tcaacttatc gtcagaaaaa ttaaaatcga atactcgtgt cactttaatt 240 caccaagata ttctacagtt tcaattccct aacaaacaga ggtataaaat tgttgggaat 300 attccttacc atttaagcac acaaattatt aaaaaagtgg tttttgaaag ccatgcgtct 360 gacatctatc tgattgttga agaaggattc tacaagcgta ccttggatat tcaccgaaca 420 ctagggttgc tcttgcacac tcaagtctcg attcagcaat tgcttaagct gccagcggaa 480 tgctttcatc ctaaaccaag agtaaacagt gtcttaataa aacttacccg ccataccaca 540 gatgttccag ataaatattg gaagctatat acgtactttg tttcaaaatg ggtcaatcga 600 gaatatcgtc aactgtttac taaaaatcag tttcatcaag caatgaaaca cgccaaagta 660 aacaatttaa gtaccgttac ttatgagcaa gtattgtcta tttttaatag ttatctatta 720 tttaacggga ggaaataa 738 115 735 DNA Staphylococcus aureus 115 atgaacgaga aaaatataaa acacagtcaa aactttatta cttcaaaaca taatatagat 60 aaaataatga caaatataag attaaatgaa catgataata tctttgaaat cggctcagga 120 aaagggcatt ttacccttga attagtacag aggtgtaatt tcgtaactgc cattgaaata 180 gaccataaat tatgcaaaac tacagaaaat aaacttgttg atcacgataa tttccaagtt 240 ttaaacaagg atatattgca gtttaaattt cctaaaaacc aatcctataa aatatttggt 300 aatatacctt ataacataag tacggatata atacgcaaaa ttgtttttga tagtatagct 360 gatgagattt atttaatcgt ggaatacggg tttgctaaaa gattattaaa tacaaaacgc 420 tcattggcat tatttttaat ggcagaagtt gatatttcta tattaagtat ggttccaaga 480 gaatattttc atcctaaacc tagagtgaat agctcactta tcagattaaa tagaaaaaaa 540 tcaagaatat cacacaaaga taaacagaag tataattatt tcgttatgaa atgggttaac 600 aaagaataca agaaaatatt tacaaaaaat caatttaaca attccttaaa acatgcagga 660 attgacgatt taaacaatat tagctttgaa caattcttat ctcttttcaa tagctataaa 720 ttatttaata agtaa 735 116 1029 DNA Enterococcus faecalis 116 atgaataaaa taaaagtcgc aattatcttc ggcggttgct cggaggaaca tgatgtgtcg 60 gtaaaatccg caatagaaat tgctgcgaac attaatactg aaaaattcga tccgcactac 120 atcggaatta caaaaaacgg cgtatggaag ctatgcaaga agccatgtac ggaatgggaa 180 gccgatagtc tccccgccat attctccccg gataggaaaa cgcatggtct gcttgtcatg 240 aaagaaagag aatacgaaac tcggcgtatt gacgtggctt tcccggtttt gcatggcaaa 300 tgcggggagg atggtgcgat acagggtctg tttgaattgt ctggtatccc ctatgtaggc 360 tgcgatattc aaagctccgc agcttgcatg gacaaatcac tggcctacat tcttacaaaa 420 aatgcgggca tcgccgtccc cgaatttcaa atgattgaaa aaggtgacaa accggaggcg 480 aggacgctta cctaccctgt ctttgtgaag ccggcacggt caggttcgtc ctttggcgta 540 accaaagtaa acagtacgga agaactaaac gctgcgatag aagcagcagg acaatatgat 600 ggaaaaatct taattgagca agcgatttcg ggctgtgagg tcggctgcgc ggtcatggga 660 aacgaggatg atttgattgt cggcgaagtg gatcaaatcc ggttgagcca cggtatcttc 720 cgcatccatc aggaaaacga gccggaaaaa ggctcagaga atgcgatgat tatcgttcca 780 gcagacattc cggtcgagga acgaaatcgg gtgcaagaaa cggcaaagaa agtatatcgg 840 gtgcttggat gcagagggct tgctcgtgtt gatctttttt tgcaggagga tggcggcatc 900 gttctaaacg aggtcaatac cctgcccggt tttacatcgt acagccgcta tccacgcatg 960 gcggctgccg caggaatcac gcttcccgca ctaattgaca gcctgattac attggcgata 1020 gagaggtga 1029 117 1031 DNA Enterococcus gallinarum 117 atgaaaaaaa ttgccgtttt atttggaggg aattctccag aatactcagt gtcactaacc 60 tcagcagcaa gtgtgatcca agctattgac ccgctgaaat atgaagtaat gaccattggc 120 atcgcaccaa caatggattg gtattggtat caaggaaacc tcgcgaatgt tcgcaatgat 180 acttggctag aagatcacaa aaactgtcac cagctgactt tttctagcca aggatttata 240 ttaggagaaa aacgaatcgt ccctgatgtc ctctttccag tcttgcatgg gaagtatggc 300 gaggatggct gtatccaagg actgcttgaa ctaatgaacc tgccttatgt tggttgccat 360 gtcgctgcct ccgcattatg tatgaacaaa tggctcttgc atcaacttgc tgataccatg 420 ggaatcgcta gtgctcccac tttgctttta tcccgctatg aaaacgatcc tgccacaatc 480 gatcgtttta ttcaagacca tggattcccg atctttatca agccgaatga agccggttct 540 tcaaaaggga tcacaaaagt aactgacaaa acagcgctcc aatctgcatt aacgactgct 600 tttgcttacg gttctactgt gttgatccaa aaggcgatag cgggtattga aattggctgc 660 ggcatcttag gaaatgagca attgacgatt ggtgcttgtg atgcgatttc tcttgtcgac 720 ggtttttttg attttgaaga gaaataccaa ttaatcagcg ccacgatcac tgtcccagca 780 ccattgcctc tcgcgcttga atcacagatc aaggagcagg cacagctgct ttatcgaaac 840 ttgggattga cgggtctggc tcgaatcgat tttttcgtca ccaatcaagg agcgatttat 900 ttaaacgaaa tcaacaccat gccgggattt actgggcact cccgctaccc agctatgatg 960 gcggaagtcg ggttatccta cgaaatatta gtagagcaat tgattgcact ggcagaggag 1020 gacaaacgat g 1031 118 809 DNA Abiotrophia adiacens 118 tggtgctatc ttagtagtat ctgcagctga tggtccaatg cctcaaacac gtgaacacat 60 cttattatca cgtcaagtag gtgttcctta catcgttgta ttcttaaaca aagttgacat 120 ggttgacgat gaagaattat tagaattagt agaaatggaa gttcgtgact tattatcaga 180 atacgatttc ccaggcgatg acactccagt tgttgcaggt tctgctttac gcgctttaga 240 aggcgacgct tcatacraag aaaaaatctt agaattaatg gctgctgttg acgaatacat 300 tccaactcca gaacgygacg ttgacaaacc attcatgatg ccagttgaag acgtgttctc 360 aatcacaggt cgtggtactg ttgctacagg tcgtgttgaa cgtggacaag ttcgtgttgg 420 tgacgaagtt gaaatcgttg gtatttcaga agaaacttca aaaacaactg taactggtgt 480 tgaaatgttc cgtaaattgt tagactacgc tgaagcaggg gataacattg gtacattatt 540 acgtggtgtt acacgtgaca acatcgaacg tggacaagtt cttgctaaac caggaacaat 600 cactccacat actaaattca aagctgaagt ttacgtatta actaaagaag aaggtggacg 660 tcatactcca ttcttctcta actaccgtcc tcaattctac ttccgtacaa cagacatcac 720 tggtgtttgt gtgttaccag aaggcgttga aatggtaatg cctggtgata acgtaactat 780 ggaagttgaa ttaattcacc cagtagcga 809 119 817 DNA Abiotrophia defectiva 119 cggcgcgatc ctcgttgtat ctgctgctga cggcccaatg ccacaaactc gtgaacacat 60 cctcttgtct cgtcaagttg gtgttcctta catcgtagta ttcttgaaca aagttgacat 120 ggttgacgac gaagaattgc tcgaattagt tgaaatggaa gttcgtgacc tcttgtctga 180 atacgacttc ccaggcgacg acactccagt tatcgctggt tcagctttga aagctttaga 240 aggcgacgct aactacgaag ctaaagtttt agaattgatg gaacaagttg atgcttacat 300 tccagaacca gaacgtgaca ctgacaagcc attcatgatg ccagtcgaag acgtattctc 360 tatcactggt cgtggtactg ttgcaactgg tcgtgttgaa cgtggtcaag ttcgcgttgg 420 tgacgaagtt gaaatcgttg gtatcgaaga agaaacttct aagactaccg ttaccggtgt 480 tgaaatgttc cgtaagttat tggattacgc tgaagctggg gacaacgttg gtaccttgtt 540 acgtggtgta actcgtgacc aaatccaacg tggtcaagta ttatctaaac caggttcaat 600 cactccgyac actaagttcg aagctgaagt gtacgtattg tctaaagaag aaggtggtcg 660 tcacactcca ttcttctcta actaccgtcc acaattctac ttccgtacaa ctgacgtaac 720 tggtgttgtt actttaccag aaggtactga aatggttatg ccaggcgaca acgtacaaat 780 ggttgttgaa ttgatccacc caatcgcgat cgaagaa 817 120 754 DNA Candida albicans 120 ctctgtcaaa tgggacaaaa acagatttga agaaatcatc aaggaaacct ccaacttcgt 60 caagaaggtt ggttacaacc caaagactgt tccattcgtt ccaatctctg gttggaatgg 120 tgacaacwtg attgaascat ccaccaactg tccatggtac aagggttggg aaaaggaaac 180 caaatccggt aaagttactg gtaagacctt gttagaagct attgacgcta ttgaaccacc 240 aaccagacca accgacaaac cattgagatt gccattrcaa gatgtttaca agatcggtgg 300 tattggtact gtgccagtcg gtagagttga aactggtatc atcaaagccg gtatggtwgt 360 tactttcgcc ccagctggtg ttaccactga agtcaartcc gttgaaatgc atcacgaaca 420 attggctgaa ggtgttccag gtgacaatgt trgtttcaac gttaagaacr tttccgttaa 480 agaaattaga agaggtaacg tttgtggtga ctccaagaac gatccaccaa agggttgtga 540 ctctttcaat gcccaagtca ttgttttgaa ccatccaggt caaatctctg ctggttactc 600 tccagtcttg gattgtcacr ctgcccacat tgcttgtaaa ttcgacrctt tggttgaaaa 660 gattgacaga agaactggta agraattgga agaaaatcca aaattcgtca aatccggtga 720 tgctgctatc gtcaagatgg tcccaaccaa acca 754 121 753 DNA Candida glabrata 121 tctgtcaagt gggatgaatc cagattcgct gaaatcgtta aggaaacctc caacttcatc 60 aagaaggtcg gttacaaccc aaagactgtt ccattcgtcc caatctctgg ttggaacggt 120 gacaacatga ttgaagccac caccaacgct tcctggtaca agggttggga aaaggaaacc 180 aaggctggtg tcgtcaaggg taagaccttg ttggaagcca ttgacgctat cgaaccacca 240 accagaccaa ctgacaagcc attgagattg ccattgcaag atgtctacaa gatcggtggt 300 atcggtacgg tgccagtcgg tagagtcgaa accggtgtca tcaagccagg tatggttgtt 360 accttcgccc cagctggtgt taccactgaa gtcaagtccg ttgaaatgca ccacgaacaa 420 ttgactgaag gtttgccagg tgacaacgtt ggtttcaacg ttaagaacgt ttccgttaag 480 gaaatcagaa gaggtaatgt ctgtggtgac tccaagaacg acccaccaaa ggctgctgct 540 tctttcaacg ctaccgtcat tgtcttgaac cacccaggtc aaatctctgc tggttactct 600 ccagttttgg actgtcacac cgcccacatt gcttgtaagt tcgaagaatt gttggaaaag 660 aacgacagaa gatccggtaa gaagttggaa gactctccaa agttcttgaa gtccggtgac 720 gctgctttgg ttaagttcgt tccatccaag cca 753 122 752 DNA Candida kruisii 122 ccgttaagtg ggatgaaaac agatttgaag aaattgtcaa ggaaacccaa aacttcatca 60 agaaggttgg ttacaaccca aagactgttc cattcgttcc aatctctggt tggaatggtg 120 acaacatgat tgaagcatcc accaactgtc catggtacaa gggttggact aaggaaacca 180 aggcaggtgt tgttaagggt aagaccttat tagaagcaat cgatgctatt gaaccacctg 240 tcagaccaac cgaaaagcca ttaagattac cattacaaga tgtttacaag attggtggta 300 ttggtactgt gccagtcggt agagtcgaaa ccggtgtcat taagccaggt atggttgtca 360 cttttgctcc agcaggtgtc accaccgaag tcaaatccgt tgaaatgcac catgaacaat 420 tagaacaagg tgttccaggt gataacgttg gtttcaacgt taagaacgty tctgtcaagg 480 atatcaagag aggtaacgtt tgtggtgact ccaagaacga cccaccaatg ggtgcagctt 540 ctttcaatgc tcaagtcatt gtcttgaacc accctggtca aatttccgct ggttactctc 600 cagtcttgga ttgtcacact gcccacattg catgtaagtt cgacgaatta atcgaaaaga 660 ttgacagaag aactggtaag tctgttgaag accatccaaa gtcygtcaag tctggtgatg 720 cagctatcgt caagatggtc ccaaccaagc ca 752 123 754 DNA Candida parapsilosis 123 ctcagtcaaa tgggacaaga rcagatacga agaaattgtc aaggaaactt ccaacttcgt 60 caagaaggtt ggttacaacc ctaaagctgt cccattcgtc ccaatctctg gttggaacgg 120 tgacaatatg attgaaccat caaccaactg tccatggtac aagggttggg aaaaggaaac 180 taaagctggt aaggttaccg gtaagacctt gttggaagct atcgatgcta tcgarccacc 240 aaccagacca actgacaagc cattgagatt gccattgcaa gatgtctaca agattggtgg 300 tattggaact gtgccagttg gtagagttga aaccggtatc atcaaggctg gtatggttgt 360 tacttttgcc ccagctggtg ttaccactga agtcaagtcc gttgaaatgc accacgaaca 420 attgactgaa ggtgtcccag gtgacaatgt tggtttcaac gtcaagaacg tttcagttaa 480 ggaaatcaga agaggtaacg tytgtggtga ctccaagaac gatccaccaa agggatgtga 540 ytccttcaat gctcaagtta ttgtcttgaa ccacccaggt caaatctctg ctggttactc 600 accagtcttg gattgtcaca ctgcccacat tgcttgtaaa ttcgacactt tgattgaaaa 660 gattgacaga agaaccggta agaaattgga agwtgaacca aaattcatca agtccggtga 720 tgctgcyatc gtcaagatgg tcccaaccaa gcca 754 124 753 DNA Candida tropicalis 124 tctgttaaat gggacaaraa cagatttgaa gaaattatca aggaaacytc taacttcgtc 60 aagaaggttg gttacaaccc taaggctgtt ccattcgttc caatctcwgg ttggaatggt 120 gacaacatga ttgaagcttc taccaactgt ccatggtaca agggttggga aaaagaaacc 180 aaggctggta aggttaccgg taagactttg ttggaagcca ttgatgctat tgaaccacct 240 tcaagaccaa ctgacaagcc attgagattg ccattgcaag atgtttacaa gattggtggt 300 attggtactg tgccagtcgg tagagttgaa actggtgtca tcaaagccgg tatggttgtt 360 actttygccc cagctggtgt taccactgaa gtcaaatccg tygaaatgca ccacgaacaa 420 ttggctgaag gtgtcccagg tgacaatgtt ggtttcaacg ttaagaacgt ttctgttaaa 480 gaaattagaa gaggtaacgt ttgtggtgac tccaagaacg atccaccaaa gggttgtgac 540 tctttcaacg ctcaagttat tgtcttgaac cacccaggtc aaatytctgc tggttactct 600 ccagtcttgg attgtcacac tgctcatatt gcttgtaaat tcgacacctt ggttgaaaag 660 attgacagaa gaactggtaa gaaattggaa gaaaatccaa aattcgtcaa atccggtgat 720 gctgctattg tcaagatggt tccaaccaaa cca 753 125 814 DNA Corynebacterium accolens 125 cggcgctatc ctggttgttg ctgcaaccga tggcccgatg ccgcagaccc gcgagcacgt 60 tctgcttgct cgccaggttg gcgttcctta catcctcgtt gcactgaaca agtgcgacat 120 ggttgatgat gaggaaatca tcgagctcgt ggagatggag atctccgagc tgctcgcaga 180 gcaggactac gatgaggaag ctcctatcgt tcacatctcc gctctgaagg cactcgaggg 240 tgacgagaag tgggtacagt ccatcgttga cctgatggat gcctgcgaca actccatccc 300 tgatccggag cgcgctaccg atcagccgtt cttgatgcct atcgaggaca tcttcaccat 360 taccggccgc ggtaccgttg ttaccggccg tgttgagcgt ggtcgtctga acgtcaacga 420 ggacgttgag atcatcggta tccaggagaa gtcccagaac accaccgtta ccggtatcga 480 gatgttccgc aagatgatgg actacaccga ggctggcgac aactgtggtc tgcttctgcg 540 tggtaccaag cgtgaggacg ttgagcgtgg ccaggttgtt atcaagccgg gcgcttacac 600 ccctcacacc aagttcgagg gttccgtcta cgtcctgaag aaggaagagg gcggccgcca 660 caccccgytc atgaacaact accgtcctca gttctacttc cgcaccaccg acgttaccgg 720 tgttgtgaac ctgcctgagg gcaccgagat ggttatgcct ggcgacaacg ttgagatgtc 780 tgttgagctc atccagcctg ttgctatgga cgag 814 126 814 DNA Corynebacterium diphtheriae 126 cggcgcaatc ctcgttgttg ctgccaccga cggcccaatg cctcagaccc gtgagcacgt 60 tctgctcgct cgccaggtcg gcgttcctta catcctcgtt gctctgaaca agtgcgacat 120 ggttgatgat gaggaaatca tcgagctcgt cgagatggag atccrtgagc tgctcgctga 180 gcaggattac gacgaagagg ctccaatcat ccacatctcc gcactgaagg ctcttgaggg 240 cgacgagaag tggacccagt ccatcatcga cctcatgcag gcttgckatg attccatccc 300 agacccagag cgtgagaccg acaagccatt cctcatgcct atcgaggaca tcttcaccat 360 caccggccgc ggtaccgttg ttaccggccg tgttgagcgt ggctccctga aggtcaacga 420 ggacgtcgag atcatcggta tccgcgagaa kgctaccacc accaccgtta ccggtatcga 480 gatgttccgt aagcttctcg actacaccga ggctggcgac aactgtggtc tgcttctccg 540 tggcgttaag cgcgaagacg ttgagcgtgg ccaggttgtt gttaagccag gcgcttacac 600 ccctcacacc gagttcgagg gctctgtcta cgttctgtcc aaggacgagg gtggccgcca 660 caccccattc ttcgacaact accgcccaca gttctacttc cgcaccaccg acgttaccgg 720 tgttgtgaag cttcctgagg gcaccgagat ggtcatgcct ggcgacaacg tcgacatgtc 780 cgtcaccctg atccagcctg tcgctatgga tgag 814 127 814 DNA Corynebacterium genitalium 127 cggcgccatc ctggttgttg ctgcaaccga tggcccgatg ccgcagaccc gtgagcacgt 60 tctgctggct cgccaggttg gcgttccgta catcctagtt gcactgaaca agtgcgacat 120 ggttgatgat gaggagctgc tggagctcgt cgagatggag gtccgcgagc tgctggctga 180 gcaggacttc gacgaggaag cacctgttgt tcacatctcc gcactgaagg ccctggaggg 240 cgacgagaag tgggctaagc agatcctgga gctcatggag gcttgcgaca actccatccc 300 ggatccggag cgcgagaccg acaagccgtt cctgatgccg gttgrggaca tcttcaccat 360 taccggccgc ggtaccgttg ttaccggccg tgttgagcgt ggcgtcctga acctgaacga 420 cgaggtcgag atcctgggca tccgcgagaa gtccaccaag accaccgtta cctccatcga 480 gatgttcaac aagctgctgg acaccgcaga ggctggcgac aacgccgcac tgctgctgcg 540 tggcctgaag cgcgaagatg ttgagcgtgg tcagatcgtt gctaagccgg gcgagtacac 600 cccgcacacc gagttcgagg gctccgtcta cgttctgtcc aaggacgagg gtggccgcca 660 caccccgttc ttcgacaact accgtccgca gttctatttc cgcaccaccg acgttaccgg 720 tgttgtgaag ctgccggagg gcaccgagat ggttatgccg ggcgacaacg ttgacatgtc 780 cgtcaccctg atccagccgg ttgctatgga cgag 814 128 814 DNA Corynebacterium jeikeium 128 cggcgccatc ctggttgttg ccgcaaccga tggcccgatg ccgcagaccc gcgagcacgt 60 tctgctggcy cgccaggttg gcgttccgta catcctggtt gcactgaaca agtgtgacat 120 ggttgacgat gaggagctgc tggagctcgt cgagatggag gtccgcgagc tgctggctga 180 gcaggacttc gacgaggaag ctccggttgt tcacatctcc gcactgaagg ccctggaggg 240 cgacgagaag tgggctaacc agattctcga gctgatgcag gcttgcgacg agtctatccc 300 ggatccggag cgcgagaccg acaagccgtt cctgatgccg gttgwggaca tcttcaccat 360 taccggtcgc ggtaccgttg ttaccggccg tgttgagcgt ggcatcctga acctgaacga 420 cgaggttgag atcctgggta tccgcgagaa gtcccagaag accaccgtta cctccatcga 480 gatgttcaac aagctgctgg acaccgcaga ggctggcrac aacgctgcac tgctgctgcg 540 tggtctgaag cgcgaggacg ttgagcgtgg ccagatcatc gctaagccgg gcgagtacac 600 cccgcacacc gagttcgagg gctccgtcta cgttctgtcc aaggacgagg gcggccgcca 660 caccccgttc ttcgacaact accgtccgca gttctacttc cgcaccaccg acgttaccgg 720 tgttgtgaag ctgcctgagg gcaccgagat ggttatgccg ggcgacaacg tygacatgtc 780 cgtcaccctg atccagccgg ttgctatgga cgag 814 129 748 DNA Corynebacterium pseudodiphtheriticum 129 cggcgctatc ttggttgttg cagctaccga cggcccaatg ccacagactc gcgagcacgt 60 tctgctggct cgccaggttg gcgttcctta catcctggtt gcactaaaca agtgcgacat 120 ggttgacgac gaggaaatcc tcgagctcgt cgagatggag atccgcgaat tgctggctga 180 ccaggaattc gacgaagaag ctccaatcgt tcacatctcc gcagtcggcg ccttggaagg 240 cgaagagagg tgggttaacg ccatcgttga actgatggat gcttgtgacg agtcgatccc 300 tgatccagac cgtgctaccg acaagccatt cctgatgcct atcgaggaca tcttcaccat 360 taccggtcgt ggcaccgttg ttacgggtcg tgttgagcgt ggttccctga aggtcaacga 420 agaagtcgag atcatcggca tcaaggaaaa gtcccagaag accaccatca ccggtatcga 480 aatgttccgc aagatgctgg actacaccga ggccggcgac aacgctggtc tgctgcttcg 540 cggtaccaag cgtgaagacg ttgagcgtgg acaggttatc gttgctccag gtgcttacag 600 cacccacaag aagttcgaag gttccgtcta cgttctttcc aaggacgagg gcggccgcca 660 caccccgttc ttcgacaact accgtcctca gttctacttc cgcaccaccg acgttaccgg 720 tgttgttacc ctgcctgagg gcaccgag 748 130 813 DNA Corynebacterium striatum 130 ggcgctatct tggttgttgc tgcaaccgat ggcccgrtgc cgcagacccg cgagcacgtt 60 cttctggctc gccaggttgg cgttccttac atcctcgttg cactgaacaa gtgcgacatg 120 gttgacgacg aggaaattat cgagctcgtc gagatggaga tccgcgaact gctcgcagag 180 caggactacg atgaggaagc tccgatcgtt cacatctctg ctctgaaggc tcttgagggc 240 grcgagaagt gggtacaggc tatcgttgac ctgatgcagg cttgcgatga ctccatcccg 300 gatccggagc gcgagctgga caagccgttc ctgatgccaa tcgaggacat cttcaccatc 360 accggccgcg gtaccgttgt tactggccgt gttgagcgtg gctccctgaa cgtcaacgag 420 gacgttgaga tcatcggtat ccaggacarg tccatctcca ccaccgttac cggtatcgag 480 atgytccgca agatgatgga ctacaccgag gctggcgaca actgtggtct gcttctgcgt 540 ggtaccaagc gtgaagaggt tgagcgcggc caggttgtta ttaagccggg cgcttacacc 600 cctcacaccc agttcgaggg ttccgtctac gtcctgaaga aggaagaggg cggccgccac 660 accccgttca tggacaacta ccgtccgcag ttctacttcc gcaccaccga cgttaccggc 720 gtcatcaagc tgcctgaggg caccgagatg gttatgcctg gcgacaacgt cgagatgtcy 780 gtcgagctga tccagccggt cgctatggac gag 813 131 817 DNA Enterococcus avium 131 cggagctatc ttagtagtat ctgctgctga tggccctatg cctcaaactc gtgaacacat 60 cttgttatct cgtaacgttg gtgttcctta catcgttgta ttcttaaaca aaatggatat 120 ggttgacgat gaagaattac ttgaattagt tgaaatggaa gttcgtgact tattaactga 180 atacgacttc ccaggcgacg acactccagt tatcgcaggt tcagcgttga aagctttaga 240 aggcgacgct tcatacgaag aaaaaatctt agaattaatg gctgctgttg acgaatatat 300 cccaacacca gttcgtgata ctgacaaacc attcatgatg ccagtcgaag acgtattctc 360 aatcactggt cgtggtactg ttgcaactgg tcgtgttgaa cgtggacaag ttcgcgttgg 420 tgacgaagtt gaaatcgtag gtatcgctga cgaaactgct aaaacaactg ttacaggtgt 480 tgaaatgttc cgtaaattgt tagactacgc tgaagcaggt gacaacatcg gtgctttgtt 540 acgtggtgtt gcacgtgaag atatccaacg tggacaagta ttggctaaac cagcttcaat 600 cactccacat acaaaattct ctgcagaagt ttatgttcta actaaagaag aaggtggacg 660 tcatactcca ttcttcacta actaccgtcc tcagttctac ttccgtacaa ctgacgtaac 720 tggtgtagtt gatctaccag aaggtactga aatggtwatg cctggggata acgtaactat 780 ggaagttgaa ttgatycacc caatygcggt agaagac 817 132 817 DNA Enterococcus faecalis 132 cggagctatc ttagtagttt ctgctgctga tggtcctatg cctcaaacac gtgaacatat 60 cttattatca cgtaacgttg gtgtaccata catcgttgta ttcttaaaca aaatggatat 120 ggttgatgac gaagaattat tagaattagt agaaatggaa gttcgtgact tattatcaga 180 atacgatttc ccaggcgatg atgttccagt tatcgcaggt tctgctttga aagctttaga 240 aggcgacgag tcttatgaag aaaaaatctt agaattaatg gctgcagttg acgaatatat 300 cccaactcca gaacgtgata ctgacaaacc attcatgatg ccagtcgaag acgtattctc 360 aatcactgga cgtggtactg ttgctacagg acgtgttgaa cgtggtgaag ttcgcgttgg 420 tgacgaagtt gaaatcgttg gtattaaaga cgaaacatct aaaacaacyg ttacaggtgt 480 tgaaatgttc cgtaaattat tagactacgc tgaagcaggc gacaacmtcg gtgctttatt 540 acgtggtgta gcacgtgaag atatcgaacg tggacaagta ttagctaaac cagctacaat 600 cactccacac acaaaattca aagctgaagt atacgtatta tcaaaagaag aaggcggacg 660 tcacactcca ttcttcacta actaccgtcc tcaattctac ttccgtacaa cagacgttac 720 tggtgttgta gaattgccag aaggtactga aatggtaatg cctggtgata acgttgctat 780 ggacgttgaa ttaattcacc caatcgctat cgaagac 817 133 774 DNA Enterococcus faecium 133 cggagctatc ttggtagttt ctgctgctga cggcccaatg cctcaaactc gtgaacacat 60 cctattgtct cgtcaagttg gtgttcctta catcgttgta ttcttgaaca aagtagacat 120 ggttgatgac gaagaattac tagaattagt tgaaatggaa gttcgtgacc tattaacaga 180 atacraattc cctggtgrcg atgttcctgt agttgctgga tcagctttga aagctctaga 240 aggcgacgct tcatacgaag aaaaaattct tgaattaatg gctgcagttg acgaatacat 300 cccaactcca gaacgtgaca acgacaaacc attcatgatg ccagttgaag acgtgttctc 360 aattactgga cgtggtactg ttgctacagg tcgtgttgaa cgtggacaag ttcgcgttgg 420 tgacgaagtt gaagttgttg gtattgctga agaaacttca aaaacaacag ttactggtgt 480 tgaaatgttc cgtaaattgt tagacyacgc tgaagctgga gacracattg gtgctttact 540 acgtggtgtt gcacgtgaag acatccaacg tggacaagtt ttagctaaac caggtacaat 600 cacacctcrt acaaaattct ctgcagaagt atacgtgttg acaaaagaag aaggtggacg 660 tcatactcca ttcttcacta actaccgtcc acaattctac ttccgtacaa ctgacgtaac 720 aggtgttgtt gaattaccag aaggaactga aatggtcatg cccggtgaca acgt 774 134 809 DNA Enterococcus gallinarum 134 cggtgcgatc ttagtagtat ctgctgctga cggtcctatg cctcaaactc gtgaacacat 60 cttgttatca cgtaacgttg gcgtaccata catcgttgtt ttcttgaaca aaatggatat 120 ggttgaygac gaagaattgc tagaattagt tgaaatggaa gttcgtgacc tattgtctga 180 atatgacttc ccaggcgacg atgttcctgt aatcgccggt tctgctttga aagctcttga 240 aggagatcct tcatacgaag aaaaaatcat ggaattgatg gctgcagttg acgaatacgt 300 tccaactcca gaacgtgata ctgacaaacc attcatgatg ccagtcgaag acgtattctc 360 aatcactgga cgtggtactg ttgctacagg ccgtgttgaa cgtggacaag ttcgcgttgg 420 tgatgaagta gaaatcgttg gtattgctga cgaaactgct aaaacaactg taacaggtgt 480 tgaaatgttc cgtaaattgt tagactatgc tgaagcaggg gataacattg gtgcattgct 540 acgtggggtt gctcgtgaag acatccaacg tggacaagta ttggctaaag ctggtacaat 600 cacacctcat acaaaattca aagctgaagt ttatgttttg acaaaagaag aaggtggacg 660 tcacactcca ttcttcacta actaccgtcc tcagttctac ttccgtacaa ctgacgtaac 720 tggtgttgtt gaattaccag aaggaactga aatggtgatg cctggcgaca acgtgaccat 780 cgacgttgaa ttgatrcacc caatcgctc 809 135 823 DNA Gardnerella vaginalis 135 tggcgcaatc ctcgtggttg ctgctaccga cggtccaatg gctcagaccc gtgaacacgt 60 cttgcttgct aagcaggtcg gcgttccaaa aattcttgtt gctttgaaca agtgcgatat 120 ggttgacgac gaagagctta tcgatctcgt tgaagaagag gtccgtgacc tcctcgaaga 180 aaacggcttc gatcgcgatt gcccagtcyt ccgtacttcc gcttacggcg ctttgcatga 240 tgacgctcca gaccacgaca agtgggtaga gaccgtcaag gaactcatga aggctgttga 300 cgagtacatc ccaaccccaa ctcacgatct tgacaagcca ttcttgatgc caatcgaaga 360 tgtgttcacc atctccggtc gtggtyccgt tgtcaccggt cgtgttgagc gtggtaagct 420 cccaatcaac accccagttg agatcgttgg tttgcgcgat acccagacca ccaccgtcac 480 ctctatcgag accttccaca agcagatgga tgaggcagag gctggcgata acactggtct 540 tcttctccgc ggtatcaacc gtaccgacgt tgagcgtggt caggttgtgg ctgctccagg 600 ttctgtgact ccacacacca agttcgaagg cgaagtttac gtcttgacca aggacgaagg 660 tggccgtcac tcgccattct tctccaacta ccgtccacag ttctacttcc gtaccaccga 720 tgttactggc gttatcacct tgccagacgg catcgaaatg gttcagccag gcgatcacgc 780 aaccttcact gttgagttga tccaggctat cgcaatggaa gag 823 136 817 DNA Listeria innocua 136 cggagctatc ttagtagtat ctgctgctga tggcccaatg ccacaaactc gtgaacatat 60 cttactttca cgtcaagttg gtgttccata catcgttgta ttcatgaaca aatgtgacat 120 ggttgacgat gaagaattac tagaattagt tgaaatggaa attcgtgatc tattaactga 180 atatgaattc cctggcgatg acattcctgt aatcaaaggt tcagctctta aagcacttca 240 aggtgaagct gactgggaag ctaaaattga cgagttaatg gaagctgtag attcttacat 300 tccaactcca gaacgtgata ctgacaaacc attcatgatg ccagttgagg atgtattctc 360 aatcactggt cgtggaacag ttgcaactgg acgtgttgaa cgtggacaag ttaaagttgg 420 tgacgaagta gaagttatcg gtattgaaga agaaagcaaa aaagtagtag taactggagt 480 agaaatgttc cgtaaattac tagactacgc tgaagctggc gacaacattg gcgcacttct 540 acgtggtgtt gctcgtgaag atatccaacg tggtcaagta ttagctaaac caggttcgat 600 tactccacac actaacttca aagctgaaac ttatgtttta actaaagaag aaggtggacg 660 tcacactcca ttcttcaaca actaccgccc acaattctat ttccgtacta ctgacgtaac 720 tggtattgtt acacttccag aaggtactga aatggtaatg cctggtgata acattgagct 780 tgcagttgaa ctaattgcac caatcgctat cgaagac 817 137 818 DNA Listeria ivanovii 137 cggagctatc ttagtagtat ctgctgctga tggtccaatg ccacaaactc gtgaacatat 60 tcttactttc acgtcaagtt ggtgttccat acatcgttgt attcatgaac aaatgtgaca 120 tggttgacga tgaagaatta cttgaattag ttgaaatgga aattcgtgat ctattaactg 180 aatatgaatt ccctggcgac gacattcctg taatcaaagg ttcagctctt aaagcacttc 240 aaggtgaagc tgattgggaa gctaaaattg acgagttaat ggaagctgta gattcttaca 300 ttccaactcc agaacgtgat actgacaaac cattcatgat gccagttgag gatgtattct 360 caatcactgg tcgtggaaca gttgcaactg gacgtgttga acgtggacaa gttaaagttg 420 gtgacgaagt agaagttatc ggtattgaag aagaaagcaa aaaagtagta gtaactggag 480 tagaaatgtt ccgtaaatta ctagactacg ctgaagctgg cgacaacatt ggcgcacttc 540 tacgtggtgt tgctcgtgaa gatatccaac gtggtcaagt attagctaaa ccaggttcga 600 ttactccaca tactaacttc aaagctgaaa cttatgtttt aactaaagaa gaaggtggac 660 gtcatactcc attcttcaac aactaccgcc cacaattcta tttccgtact actgacgtaa 720 ctggtattgt tacacttcca gaaggtactg aaatggtaat gcctggtgat aacattgagc 780 ttgcagttga actaattgca ccaatcgcta tcgaagac 818 138 817 DNA Listeria monocytogenes 138 cggagctatc ttagtagtat ctgctgctga tggcccaatg ccacaaactc gtgaacatat 60 cttactttca cgtcaagttg gtgttccata catcgttgta ttcatgaaca aatgtgacat 120 ggttgacgat gaagaattac tagaattagt tgaaatggaa attcgtgatc tattaactga 180 atatgaattc cctggcgatg acattcctgt aatcaaaggt tcagctctta aagcacttca 240 aggtgaagct gactgggaag ctaaaattga cgagttaatg gaagctgtag attcttacat 300 tccaactccw gaacgtgata ctgacaaacc attcatgatg ccagttgagg atgtattctc 360 aatcactggt cgtggaacag ttgcaactgg acgtgttgaa cgtggacaag ttaaagttgg 420 tgacgaagta gaagttatcg gtatcgaaga agaaagcaaa aaagtagtag taactggagt 480 agaaatgttc cgtaaattac tagactacgc tgaagctggc gacaacattg gcgcacttct 540 acgtggtgtt gctcgtgaag atatccaacr tggtcaagta ttagctaaac caggttcgat 600 tactccacac actaacttca aagctgaaac ttatgtttta actaaagaag aaggtggacg 660 tcacactcca ttcttcaaca actaccgccc acaattctat ttccgtacta ctgacgtaac 720 tggtattgtt acacttccag aaggtactga aatggtaayg cctggtgata acattgagct 780 tgcagttgaa ctaattgcac caatcgctat cgaagac 817 139 817 DNA Listeria seeligeri 139 cggagctatc ttagtagtat ctgctgctga tggcccaatg ccacaaactc gtgaacatat 60 cttactttca cgtcaagttg gtgttccata catcgttgta ttcatgaaca aatgtgacat 120 ggttgacgat gaagaattac ttgaattagt tgaaatggaa attcgtgatc tattaactga 180 atatgaattc cctggtgatg acattcctgt aatcaaaggt tcagctctta aagcacttca 240 aggtgaagct gactgggaag ctaaaattga cgagttaatg gaagctgtag attcttacat 300 tccaactcca gaacgtgata ctgacaaacc attcatgatg ccagttgagg atgtattctc 360 aatcactggt cgtggaactg ttgcaactgg acgtgttgaa cgtggacaag ttaaagttgg 420 tgacgaagta gaagttatcg gtattgaaga agaaagcaaa aaagtaatag taactggagt 480 agaaatgttc cgtaaattac tagactacgc tgaagctggc gacaacattg gcgcacttct 540 acgtggtgtt gctcgtgaag atatccaacg tggtcaagta ttagctaaac caggttcgat 600 tactccacat actaacttca aagctgaaac ttatgtttta actaaagaag aaggtggacg 660 tcacactcca ttcttcaaca actaccgccc acaattctat ttccgtacta ctgacgtaac 720 tggtattgtt acacttccag aaggtactga aatggtaatg cctggtgata acattgagct 780 tgcagttgaa ctaattgcac caatcgctat cgaagac 817 140 814 DNA Staphylococcus aureus 140 cggtggtatc ttagtagtat ctgctgctga cggtccaatg ccacaaactc gtgaacacat 60 tcttttatca cgtaacgttg gtgtaccagc attagtagta ttcttaaaca aagttgacat 120 ggttgacgat gaagaattat tagaattagt agaaatggaa gttcgtgact tattaagcga 180 atatgacttc ccaggtgacg atgtacctgt aatcgctggt tcagcattar aagctttaga 240 aggcgatgct caatacgaag aaaaaatctt agaattartg gaagctgtag atacttacat 300 tccaactcca gaacgtgatt ctgacaaacc attcatgatg ccagttgagg acgtattctc 360 aatcactggt cgtggtactg ttgctacagg ccgtgttgaa cgtggtcaaa tcaaagttgg 420 tgaagaagtt gaaatcatcg gtttacatga cacatctaaa acaactgtta caggtgttga 480 aatgttccgt aaattattag actacgctga agctggtgac aacattggtg cattattacg 540 tggtgttgct cgtgaagacg tacaacgtgg tcaagtatta gctgctcctg gttcaattac 600 accacatact gaattcaaag cagaagtata cgtattatca aaagacgaag gtggacgtca 660 cactccattc ttctcaaact atcgtccaca attctatttc cgtactactg acgtaactgg 720 tgttgttcac ttaccagaag gtactgaaat ggtaatgcct ggtgataacg ttgaaatgac 780 agtagaatta atcgctccaa tcgcgattga agac 814 141 814 DNA Staphylococcus epidermidis 141 cggcggtatc ttagttgtat ctgctgctga cggtccaatg ccacaaactc gtgaacacat 60 cttattatca cgtaacgttg gtgtaccagc attagttgta ttcttaaaca aagttgacat 120 ggtagacgac gaagaattat tagaattagt tgaaatggaa gttcgtgact tattaagcga 180 atatgacttc ccaggtgacg atgtacctgt aatcgctggt tctgcattaa aagcattaga 240 aggcgatgct gaatacgaac aaaaaatctt agacttaatg caagcagttg atgattacat 300 tccaactcca gaacgtgatt ctgacaaacc attcatgatg ccagttgagg acgtattctc 360 aatcactggt cgtggtactg ttgctacagg ccgtgttgaa cgtggtcaaa tcaaagtwgg 420 tgaagaagtt gaaatcatcg gtatgcacga aacttctaaa acaactgtta ctggtgtaga 480 aatgttccgt aaattattag actacgctga agctggtgac aacatcggtg ctttattacg 540 tggtgttgca cgtgaagacg tacaacgtgg tcaagtatta gctgctcctg gttctattac 600 accacacaca aaattcaaag ctgaagtata cgtattatct aaagatgaag gtggacgtca 660 cactccattc ttcactaact atcgcccaca attctatttc crtactactg acgtaactgg 720 tgttgtaaac ttaccagaag gtacagaaat ggttatgcct ggcgacaacg ttgaaatgac 780 agttgaatta atcgctccaa tcgctatcga agac 814 142 817 DNA Staphylococcus saprophyticus 142 cggagctatc ttagtagtat ctgctgctga tggcccaatg ccacaaactc gtgaacacat 60 tcttttatca cgtracgttg gtgytccagc attagttgta ttcttaaaca aagttgacat 120 ggttgacgay gaagaattat tagaattrgt agaaatggaa gttcgtgrct tattaagcga 180 atatgacttc ccaggtgacg atgtacctgt aatctctggt tctgcattaa aagctttaga 240 aggcgacgct gactatgagc aaaaaatctt agacttaatg caagctgttg atgactycat 300 tccaacacca gaacgtgatt ctgacaaacc attcatgatg ccagttgagg acgtattctc 360 aatcactggt cgtggtactg ttgctacagg ccgtgttgaa cgtggtcaaa tcaaagtcgg 420 tgaagaaatc garatcatcg gtatgcaaga agaatcaagc aaaacaactg ttactggtgt 480 agaaatgttc cgtaaattat tagactacgc tgaagctggt gacaacattg gtgcattatt 540 acgtggtgtt tcacgtgatg atgtacaacg tggtcaagtt ttagctgctc ctggtactat 600 cacaccacat acaaaattca aagcggatgt ttacgtttta tctaaagatg aaggtggtcg 660 tcatacgcca ttcttcacta actaccgccc acaattctat ttccgtacta ctgacgtaac 720 tggtgttgtt aacttaccag aaggtactga aatggttatg cctggcgata acgttgaaat 780 ggatgttgaa ttaatttctc caatcgctat tgaagac 817 143 817 DNA Staphylococcus simulans 143 cggcggtatc ttagtagtat ctgctgcaga tggtccaatg ccacaaactc gtgaacacat 60 cttattatca cgtaacgttg gtgtaccagc tttagttgta ttcttaaaca aagctgacat 120 ggttgacgac gaagaattat tagaattagt tgaaatggaa gttcgtgact tattatctga 180 atacgacttc cctggtgacg atgtaccagt tatcgttggt tctgcattaa aagctttaga 240 aggcgaccca gaatacgaac aaaaaatctt agacttaatg caagctgtag atgactacat 300 cccaactcca gaacgtgact ctgataaacc attcatgatg ccagttgagg acgtattctc 360 aatcactggt cgtggtactg tagcaacagg ccgtgttgaa cgtggtcaaa tcaaagtcgg 420 tgaagaagtt gaaatcatcg gtatcactga agaaagcaag aaaacaacag ttacaggtgt 480 agaaatgttc cgtaaattat tagactacgc tgaagctggt gacaacatcg gtgctttatt 540 acgtggtgtt gcacgtgaag acgtacaacg tggacaagta ttagcagctc ctggctctat 600 tactccacac acaaaattca aagctgatgt ttacgtttta tctaaagaag aaggtggacg 660 tcatactcca ttcttcacta actaccgccc acaattctac ttccgtacta ctgacgtaac 720 tggcgttgtt cacttaccag aaggtactga aatggttatg cctggcgata acgtagaaat 780 gactgttgaa ttgatcgctc caatcgcgat tgaagac 817 144 817 DNA Streptococcus agalactiae 144 cggagctatc cttgtagttg cttcaactga tggaccaatg ccacaaactc gtgagcacat 60 ccttctttca cgtcaagttg gtgttaaaca ccttatcgta ttcatgaaca aagttgacct 120 tgttgatgat gaagaattgc ttgaattggt tgaaatggaa attcgtgacc ttctttcaga 180 atacgacttc ccaggtgatg accttccagt tatccaaggt tcagctctta aagcacttga 240 aggcgacgaa aaatacgaag acatcatcat ggaattgatg agcactgttg atgagtacat 300 tccagaacca gaacgtgata ctgacaaacc tttacttctt ccagttgaag atgtattctc 360 aatcactgga cgtggtacag ttgcttcagg acgtatcgac cgtggtactg ttcgtgtcaa 420 cgacgaagtt gaaatcgttg gtattaaaga agatatccaa aaagcagttg ttactggtgt 480 tgaaatgttc cgtaaacaac ttgacgaagg tcttgcaggg gacaacgttg gtgttcttct 540 tcgtggtgtt caacgtgatg aaatcgaacg tggtcaagtt cttgctaaac caggttcaat 600 caacccacac actaaattta aaggtgaagt ttacatcctt tctaaagaag aaggtggacg 660 tcatactcca ttcttcaaca actaccgtcc acaattctac ttccgtacaa ctgacgtaac 720 aggttcaatc gaacttccag caggaacaga aatggttatg cctggtgata acgttactat 780 cgaagttgaa ttgattcacc caatcgccgt agaacaa 817 145 817 DNA Streptococcus pneumoniae 145 cggagctatc cttgtagtag cttcaactga cggaccaatg ccacaaactc gtgagcacat 60 ccttctttca cgtcaggttg gtgttaaaca ccttatcgtc ttcatgaaca aagttgactt 120 ggttgacgac gaagaattgc ttgaattggt tgaaatggaa atccgtgacc tattgtcaga 180 atacgacttc ccaggtgacg atcttccagt tatccaaggt tcagcactta aagctcttga 240 aggtgactct aaatacgaag acatcgttat ggaattgatg aacacagttg atgagtatat 300 cccagaacca gaacgtgaca ctgacaaacc attgcttctt ccagtcgagg acgtattctc 360 aatcactgga cgtggtacag ttgcttcagg acgtatcgac cgtggtatcg ttaaagtcaa 420 cgacgaaatc gaaatcgttg gtatcaaaga agaaactcra aaagcagttg ttactggtgt 480 tgaaatgttc cgtaaacaac ttgacgaagg tcttgctgga gataacgtag gtgtccttct 540 tcgtggtgtt caacgtgatg aaatcgaacg tggacaagtt atcgctaaac caggttcaat 600 caacccacac actaaattca aaggtgaagt ctacatcctt actaaagaag aaggtggacg 660 tcacactcca ttcttcaaca actaccgtcc acaattctac ttccgtacta ctgacgttac 720 aggttcaatc gaacttccag caggtactga aatggtaatg cctggtgata acgtgacaat 780 cgacgttgag ttgattcacc caatcgccgt agaacaa 817 146 817 DNA Streptococcus salivarius 146 cggtgcgatc cttgtagtag catctactga cggaccaatg ccacaaactc gtgagcacat 60 ccttctttca cgtcaggttg gtgttaaaca ccttatcgtc ttcatgaaca aagttgactt 120 ggttgacgat gaagaattgc ttgaattggt tgaaatggaa atccgtgacc ttctttcaga 180 atacgatttc ccaggtgatg acattccagt tatccaaggt tcagctctta aagctcttga 240 aggtgattct aaatacgaag acatcatcat ggacttgatg aacactgttg acgaatacat 300 cccagaacca gaacgtgaca ctgacaaacc attgttgctt ccagtcgaag acgtattctc 360 aatcactggt cgtggtactg ttgcttcagg acgtatcgac cgtggtgttg ttcgtgtcaa 420 tgacgaagtt gaaatcgttg gtcttaaaga agacatccaa aaagcagttg ttactggtgt 480 tgaaatgttc cgtaaacaac ttgacgragg tattgccgga gataacgtcg gtgttcttct 540 tcgtggtatc caacgtgatg aaatcgaacg tggtcaagta ttggctgcac ctggttcaat 600 caacccacac actaaattca aaggtgaagt ttacatcctt tctaaagaag aaggtggacg 660 tcacactcca ttcttcaaca actaccgtcc acagttctac ttccgtacaa ctgacgtaac 720 aggttcaatc gaacttcctg caggtactga aatggttatg cctggtgata acgtgactat 780 cgacgttgag ttgatccacc caatcgccgt tgaacaa 817 147 897 DNA Agrobacterium tumefaciens 147 aacatgatca ccggtgctgc cgagatggac ggcgcgatcc tggtttgctc ggctgccgac 60 ggcccgatgc cacagacccg cgagcacatc ctgcttgccc gtcaggtggg cgttccggcc 120 atcgtcgtgt tcctcaacaa ggtcgaccag gttgacgacg ccgagcttct cgagctcgtc 180 gagcttgaag ttcgcgaact tctgtcgtcc tacgacttcc cgggcgacga tatcccgatc 240 atcaagggtt cggcacttgc tgctcttgaa gattctgaca agaagatcgg tgaagacgcg 300 atccgcgagc tgatggctgc tgtcgacgcc tacatcccga cgcctgagcg tccgatcgac 360 cagccgttcc tgatgccgat cgaagacgtg ttctcgatct cgggtcgtgg tacggttgtg 420 acgggtcgcg ttgagcgcgg tatcgtcaag gttggtgaag aagtcgaaat cgtcggcatc 480 cgtccgacct cgaagacgac tgttaccggc gttgaaatgt tccgcaagct gctcgaccag 540 ggccaggccg gcgacaacat cggtgcactc gttcgcggcg ttacccgtga cggcgtcgag 600 cgtggtcaga tcctgtgcaa gccgggttcg gtcaagccgc acaagaagtt catggcagaa 660 gcctacatcc tgacgaagga agaaggcggc cgtcatacgc cgttcttcac gaactaccgt 720 ccgcagttct acttccgtac gactgacgtt accggtatcg tttcgcttcc tgaaggcacg 780 gaaatggtta tgcctggcga caacgtcact gttgaagtcg agctgatcgt tccgatcgcg 840 atggaagaaa agctgcgctt cgctatccgc gaaggcggcc gtaccgtcgg cgccggc 897 148 885 DNA Bacillus subtilis 148 atgatcactg gtgctgcgca aatggacgga gctatccttg tagtatctgc tgctgatggc 60 ccaatgccac aaactcgtga gcacatcctt ctttctaaaa acgttggtgt accatacatc 120 gttgtattct taaacaaatg cgacatggta gacgacgaag agcttcttga actagttgaa 180 atggaagttc gcgatcttct tagcgaatac gacttccctg gtgatgatgt accagttgtt 240 aaaggttctg ctcttaaagc tcttgaagga gacgctgagt gggaagctaa aatcttcgaa 300 cttatggatg cggttgatga gtacatccca actccagaac gcgacactga aaaaccattc 360 atgatgccag ttgaggacgt attctcaatc actggtcgtg gtacagttgc tactggccgt 420 gtagaacgcg gacaagttaa agtcggtgac gaagttgaaa tcatcggtct tcaagaagag 480 aacaagaaaa caactgttac aggtgttgaa atgttccgta agcttcttga ttacgctgaa 540 gctggtgaca acattggtgc ccttcttcgc ggtgtatctc gtgaagaaat ccaacgtggt 600 caagtacttg ctaaaccagg tacaatcact ccacacagca aattcaaagc tgaagtttac 660 gttctttcta aagaagaggg tggacgtcat actccattct tctctaacta ccgtcctcag 720 ttctacttcc gtacaactga cgtaactggt atcatccatc ttccagaagg cgtagaaatg 780 gttatgcctg gagataacac tgaaatgaac gttgaactta tttctacaat cgctatcgaa 840 gaaggaactc gtttctctat tcgtgaaggc ggacgtactg ttggt 885 149 882 DNA Bacteroides fragilis 149 atggttactg gtgctgctca gatggacggt gctatcattg tagttgctgc tactgatggt 60 ccgatgcctc agactcgtga gcacatcctt ttggctcgtc aggtaaacgt tccgaagctg 120 gttgtattca tgaacaagtg cgatatggtt gaagatgctg agatgttgga acttgttgaa 180 atggaaatga gagaattgct ttcattctat gatttcgacg gtgacaatac tccgatcatt 240 cagggttctg ctcttggtgc attgaacggc gtagaaaaat gggaagacaa agtaatggaa 300 ctgatggaag ctgttgatac ttggattcca ctgcctccgc gcgatgttga taaacctttc 360 ttgatgccgg tagaagacgt gttctctatc acaggtcgtg gtactgtagc tacaggtcgt 420 atcgaaactg gtgttatcca tgtaggtgat gaaatcgaaa tcctcggttt gggtgaagat 480 aagaaatcag ttgtaacagg tgttgaaatg ttccgcaaac ttctggatca gggtgaagct 540 ggtgacaacg taggtctgtt gcttcgtggt gttgacaaga acgaaatcaa acgtggtatg 600 gttctttgta aaccgggtca gattaaacct cactctaaat tcaaagcaga ggtttatatc 660 ctgaagaaag aagaaggtgg tcgtcacact ccattccata acaaatatcg tcctcagttc 720 tacctgcgta ctatggactg tacaggtgaa atcactcttc cggaaggaac tgaaatggta 780 atgccgggtg ataacgtaac tatcactgta gagttgatct atccggttgc actgaacatc 840 ggtcttcgtt tcgctatccg cgaaggtgga cgtacagtag gt 882 150 888 DNA Borrelia burgdorferi 150 aatatgatta caggagcagc tcaaatggat gcagcgatac ttttagttgc tgctgatagt 60 ggtgctgagc ctcaaacaaa agagcatttg cttcttgctc aaagaatggg aataaagaaa 120 ataatagttt ttttaaataa attggactta gcagatcctg aacttgttga gcttgttgaa 180 gttgaagttt tagaacttgt tgaaaaatat ggcttttcag ctgatactcc aataatcaaa 240 ggttcagctt ttggggctat gtcaaatcca gaagatcctg aatctacaaa atgcgttaaa 300 gaacttcttg aatctatgga taattatttt gatcttccag aaagagatat tgacaagcca 360 tttttgcttg ctgttgaaga tgtattttct atttcaggaa gaggcactgt tgctactggg 420 cgtattgaaa gaggtattat taaagttggt caagaagttg aaatagttgg aattaaagaa 480 accagaaaaa ctactgttac tggtgttgaa atgttccaga aaattcttga gcaaggtcaa 540 gcaggggata atgttggtct tcttttgaga ggcgttgata aaaaagacat tgagaggggg 600 caagttttgt cagctccagg tacaattact ccacacaaga aatttaaagc ttcaatttat 660 tgtttgacta aagaagaagg cggtaggcac aagccatttt tcccagggta tagaccacag 720 ttctttttta gaacaaccga tgttactgga gttgttgctt tagagggcaa agaaatggtt 780 atgcctggtg ataatgttga tattattgtt gagctgatct cttcaatagc tatggataag 840 aatgtagaat ttgctgttcg agaaggtgga agaaccgttg cttcagga 888 151 894 DNA Brevibacterium linens 151 aacatgatca ccggtgccgc tcagatggac ggtgcgatcc tcgtcgtcgc cgctaccgac 60 ggaccgatgc cccagacccg tgagcacgtg ctgctcgcgc gtcaggtcgg cgttccctac 120 atcgtcgtgg ctctgaacaa gtccgacatg gtcgatgacg aggagctcct cgagctcgtc 180 gaattcgagg tccgcgacct gctctcgagc caggacttcg acggagacaa cgctccggtc 240 attccggtgt ccgctctcaa ggcgctggaa ggcgacgaga agtgggtcaa gagcgttcag 300 gatctcatgg ctgccgtcga tgacaacgtt ccggagccgg agcgcgatgt cgacaagccg 360 ttcctcatgc ccgtcgagga cgtcttcacg atcaccggtc gtggaaccgt cgtcaccggt 420 cgtgtcgagc gcggcgtgct cctgcctaac gacgaaatcg aaatcgtcgg catcaaggag 480 aagtcgtcca agacgactgt caccgctatc gagatgttcc gcaagaccct gccggatgcc 540 cgtgcaggtg agaacgtcgg tctgctcctc cgcggcacca agcgcgagga tgttgagcgc 600 ggtcaggtca tcgtgaagcc gggttcgatc accccgcaca ccaagttcga ggctcaggtc 660 tacatcctga gcaaggacga gggcggacgt cacaacccgt tctactcgaa ctaccgtccg 720 cagttctact tccggaccac ggacgtcacc ggtgtcatca cgctgcccga gggcaccgag 780 atggtcatgc ccggcgacaa caccgatatg tcggtcgagc tcatccagcc gatcgctatg 840 gaggaccgcc tccgcttcgc aatccgcgaa ggtggccgca ccgtcggcgc cggt 894 152 888 DNA Burkholderia cepacia 152 atgatcacgg gcgcagcgca gatggacggc gcgatcctgg tttgctcggc agcagacggc 60 ccgatgccgc aaacgcgtga gcacatcctg ctggcgcgtc aggttggtgt tccgtacatc 120 atcgtgttcc tgaacaagtg cgacagtgtg gacgacgctg aactgctcga gctggtcgag 180 atggaagttc gcgaactcct gtcgaagtac gacttcccgg gcgacgacac gccgatcgtg 240 aagggttcgg ccaagctggc gctggaaggc gacacgggcg agctgggcga agtggcgatc 300 atgagcctgg cagacgcgct ggacacgtac atcccgacgc cggagcgtgc agttgacggc 360 gcgttcctga tgccggtgga agacgtgttc tcgatctcgg gccgtggtac ggtggtgacg 420 ggtcgtgtcg agcgcggcat cgtgaaggtc ggcgaagaaa tcgaaatcgt cggtatcaag 480 ccgacggtga agacgacctg cacgggcgtt gaaatgttcc gcaagctgct ggaccaaggt 540 caggcaggcg acaacgtcgg tatcctgctg cgcggcacga agcgtgaaga cgtggagcgt 600 ggccaggttc tggcgaagcc gggttcgatc acgccgcaca cgcacttcac ggctgaagtg 660 tacgtgctga gcaaggacga aggcggccgt cacacgccgt tcttcaacaa ctaccgtccg 720 cagttctact tccgtacgac ggacgtgacg ggctcgatcg agctgccgaa ggacaaggaa 780 atggtgatgc cgggcgacaa cgtgtcgatc acggtgaagc tgattgctcc gatcgcgatg 840 gaagaaggtc tgcgcttcgc aatccgtgaa ggcggccgta cggtcggc 888 153 891 DNA Chlamydia trachomatis 153 aacatgatca ccggtgcggc tcaaatggac ggggctattc tagtagtttc tgcaacagac 60 ggagctatgc ctcaaactaa agagcatatt cttttggcaa gacaagttgg ggttccttac 120 atcgttgttt ttctcaataa aattgacatg atttccgaag aagacgctga attggtcgac 180 ttggttgaga tggagttggc tgagcttctt gaagagaaag gatacaaagg gtgtccaatc 240 atcagaggtt ctgctctgaa agctttggaa ggagatgctg catacataga gaaagttcga 300 gagctaatgc aagccgtcga tgataatatc cctactccag aaagagaaat tgacaagcct 360 ttcttaatgc ctattgagga cgtgttctct atctccggac gaggaactgt agtaactgga 420 cgtattgagc gtggaattgt taaagtttcc gataaagttc agttggtcgg tcttagagat 480 actaaagaaa cgattgttac tggggttgaa atgttcagaa aagaactccc agaaggtcgt 540 gcaggagaga acgttggatt gctcctcaga ggtattggta agaacgatgt ggaaagagga 600 atggttgttt gcttgccaaa cagtgttaaa cctcatacac agtttaagtg tgctgtttac 660 gttctgcaaa aagaagaagg tggacgacat aagcctttct tcacaggata tagacctcaa 720 ttcttcttcc gtacaacaga cgttacaggt gtggtaactc tgcctgaggg agttgagatg 780 gtcatgcctg gggataacgt tgagtttgaa gtgcaattga ttagccctgt ggctttagaa 840 gaaggtatga gatttgcgat tcgtgaaggt ggtcgtacaa tcggtgctgg a 891 154 891 DNA Escherichia coli 154 aacatgatca ccggtgctgc gcagatggac ggcgcgatcc tggtagttgc tgcgactgac 60 ggcccgatgc cgcagactcg tgagcacatc ctgctgggtc gtcaggtagg cgttccgtac 120 atcatcgtgt tcctgaacaa atgcgacatg gttgatgacg aagagctgct ggaactggtt 180 gaaatggaag ttcgtgaact tctgtctcag tacgacttcc cgggcgacga cactccgatc 240 gttcgtggtt ctgctctgaa agcgctggaa ggcgacgcag agtgggaagc gaaaatcctg 300 gaactggctg gcttcctgga ttcttacatt ccggaaccag agcgtgcgat tgacaagccg 360 ttcctgctgc cgatcgaaga cgtattctcc atctccggtc gtggtaccgt tgttaccggt 420 cgtgtagaac gcggtatcat caaagttggt gaagaagttg aaatcgttgg tatcaaagag 480 actcagaagt ctacctgtac tggcgttgaa atgttccgca aactgctgga cgaaggccgt 540 gctggtgaga acgtaggtgt tctgctgcgt ggtatcaaac gtgaagaaat cgaacgtggt 600 caggtactgg ctaagccggg caccatcaag ccgcacacca agttcgaatc tgaagtgtac 660 attctgtcca aagatgaagg cggccgtcat actccgttct tcaaaggcta ccgtccgcag 720 ttctacttcc gtactactga cgtgactggt accatcgaac tgccggaagg cgtagagatg 780 gtaatgccgg gcgacaacat caaaatggtt gttaccctga tccacccgat cgcgatggac 840 gacggtctgc gtttcgcaat ccgtgaaggc ggccgtaccg ttggcgcggg c 891 155 891 DNA Fibrobacter succinogenes 155 aacatggtga ctggtgctgc tcagatggac ggcgctatcc tcgttgttgc cgctactgac 60 ggtccgatgc cgcagactcg cgaacacatc cttctcgctc accaggttgg cgtgccgaag 120 atcgtcgtgt tcatgaacaa gtgcgacatg gttgacgatg ctgaaattct cgacctcgtc 180 gaaatggaag ttcgcgaact cctctccaag tatgacttcg acggtgacaa caccccgatc 240 atccgtggtt ccgctctcaa ggccctcgaa ggcgatccgg aataccagga caaggtcatg 300 gaactcatga acgcttgcga cgaatacatc ccgctcccgc agcgcgatac cgacaagccg 360 ttcctcatgc cgatcgaaga cgtgttcacg attactggcc gcggcactgt cgctactggc 420 cgtatcgaac gcggtgtcgt tcgcttgaac gacaaggttg aacgtatcgg tctcggtgaa 480 accaccgaat acgtcatcac cggtgttgaa atgttccgta agctcctcga cgacgctcag 540 gcaggtgaca acgttggtct cctcctccgt ggtgctgaaa agaaggacat cgtccgtggc 600 atggttctcg cagctccgaa gtctgtcact ccgcacaccg aatttaaggc tgaaatctac 660 gttctcacga aggacgaagg tggccgtcac acgccgttca tgaatggcta ccgtccgcag 720 ttctacttcc gcaccaccga cgttactggt acgatccagc tcccggaagg tgtcgaaatg 780 gttactccgg gtgacacggt cacgatccac gtgaacctca tcgctccgat cgctatggaa 840 aagcagctcc gcttcgctat ccgtgaaggt ggacgtactg ttggtgctgg c 891 156 894 DNA Flavobacterium ferrugineum 156 aacatgatca ccggtgctgc ccagatggac ggtgctatct tagttgtggc tgcatcagac 60 ggtcctatgc ctcaaacaaa agaacacatc ctgcttgctg cccaggtagg tgtacctaaa 120 atggttgtgt ttctgaataa agttgacctc gttgacgacg aagagctcct ggagctggtt 180 gagatcgagg ttcgcgaaga actgactaaa cgcggtttcg acggcgacaa cactccaatc 240 atcaaaggtt ccgctacagg cgccctcgct ggtgaagaaa agtgggttaa agaaattgaa 300 aacctgatgg acgctgttga cagctacatc ccactgcctc ctcgtccggt tgatctgccg 360 ttcctgatga gcgtagagga cgtattctct atcactggtc gtggtactgt tgctaccggt 420 cgtatcgagc gtggccgtat caaagttggt gagcctgttg agatcgtagg tctgcaggag 480 tctcccctga actctaccgt tacaggtgtt gagatgttcc gcaaactcct cgacgaaggt 540 gaagctggtg ataacgccgg tctcctcctc cgtggtgttg aaaaaacaca gatccgtcgc 600 ggtatggtaa tcgttaaacc cggttccatc actccgcaca cggacttcaa aggcgaagtt 660 tacgtactga gcaaagacga aggtggccgt cacactccat tcttcaacaa ataccgtcct 720 caattctact tccgtacaac tgacgttaca ggtgaagtag aactgaacgc aggaacagaa 780 atggttatgc ctggtgataa caccaacctg accgttaaac tgatccaacc gatcgctatg 840 gaaaaaggtc tgaaattcgc gatccgcgaa ggtggccgta ccgtaggtgc agga 894 157 891 DNA Haemophilus influenzae 157 aatatgatta ctggtgcggc acaaatggat ggtgctattt tagtagtagc agcaacagat 60 ggtcctatgc cacaaactcg tgaacacatc ttattaggtc gccaagtagg tgttccatac 120 atcatcgtat tcttaaacaa atgcgacatg gtagatgacg aagagttatt agaattagtc 180 gaaatggaag ttcgtgaact tctatctcaa tatgacttcc caggtgacga tacaccaatc 240 gtacgtggtt cagcattaca agcgttaaac ggcgtagcag aatgggaaga aaaaatcctt 300 gagttagcaa accacttaga tacttacatc ccagaaccag aacgtgcgat tgaccaaccg 360 ttccttcttc caatcgaaga tgtgttctca atctcaggtc gtggtactgt agtaacaggt 420 cgtgtagaac gaggtattat ccgtacaggt gatgaagtag aaatcgtcgg tatcaaagat 480 acagcgaaaa ctactgtaac gggtgttgaa atgttccgta aattacttga cgaaggtcgt 540 gcaggtgaaa acatcggtgc attattacgt ggtaccaaac gtgaagaaat cgaacgtggt 600 caagtattag cgaaaccagg ttcaatcaca ccacacactg acttcgaatc agaagtgtac 660 gtattatcaa aagatgaagg tggtcgtcat actccattct tcaaaggtta ccgtccacaa 720 ttctatttcc gtacaacaga cgtgactggt acaatcgaat taccagaagg cgtggaaatg 780 gtaatgccag gcgataacat caagatgaca gtaagcttaa tccacccaat tgcgatggat 840 caaggtttac gtttcgcaat ccgtgaaggt ggccgtacag taggtgcagg c 891 158 906 DNA Helicobacter pylori 158 aacatgatca ccggtgcggc gcaaatggac ggagcgattt tggttgtttc tgcagctgat 60 ggccctatgc ctcaaactag ggagcatatc ttattgtctc gtcaagtagg cgtgcctcac 120 atcgttgttt tcttaaacaa acaagacatg gtagatgacc aagaattgtt agaacttgta 180 gaaatggaag tgcgcgaatt gttgagcgcg tatgaatttc ctggcgatga cactcctatc 240 gtagcgggtt cagctttaag agctttagaa gaagcaaagg ctggtaatgt gggtgaatgg 300 ggtgaaaaag tgcttaaact tatggctgaa gtggatgcct atatccctac tccagaaaga 360 gacactgaaa aaactttctt gatgccggtt gaagatgtgt tctctattgc gggtagaggg 420 actgtggtta caggtaggat tgaaagaggc gtggtgaaag taggcgatga agtggaaatc 480 gttggtatca gacctacaca aaaaacgact gtaaccggtg tagaaatgtt taggaaagag 540 ttggaaaaag gtgaagccgg cgataatgtg ggcgtgcttt tgagaggaac taaaaaagaa 600 gaagtggaac gcggtatggt tctatgcaaa ccaggttcta tcactccgca caagaaattt 660 gagggagaaa tttatgtcct ttctaaagaa gaaggcggga gacacactcc attcttcacc 720 aattaccgcc cgcaattcta tgtgcgcaca actgatgtga ctggctctat cacccttcct 780 gaaggcgtag aaatggttat gcctggcgat aatgtgaaaa tcactgtaga gttgattagc 840 cctgttgcgt tagagttggg aactaaattt gcgattcgtg aaggcggtag gaccgttggt 900 gctggt 906 159 891 DNA Micrococcus luteus 159 aacatgatca ccggcgccgc tcagatggac ggcgcgatcc tcgtggtcgc cgctaccgac 60 ggcccgatgg cccagacccg tgagcacgtg ctcctggccc gccaggtcgg cgtgccggcc 120 ctgctcgtgg ccctgaacaa gtcggacatg gtggaggacg aggagctcct cgagcgtgtc 180 gagatggagg tccggcagct gctgtcctcc aggagcttcg acgtcgacga ggccccggtc 240 atccgcacct ccgctctgaa ggccctcgag ggcgaccccc agtgggtcaa gtccgtcgag 300 gacctcatgg atgccgtgga cgagtacatc ccggacccgg tgcgcgacaa ggacaagccg 360 ttcctgatgc cgatcgagga cgtcttcacg atcaccggcc gtggcaccgt ggtgaccggt 420 cgcgccgagc gcggcaccct gaagatcaac tccgaggtcg agatcgtcgg catccgcgac 480 gtgcagaaga ccactgtcac cggcatcgag atgttccaca agcagctcga cgaggcctgg 540 gccggcgaga actgcggtct gctcgtgcgc ggtctgaagc gcgacgacgt cgagcgcggc 600 caggtgctgg tggagccggg ctccatcacc ccgcacacca acttcgaggc gaacgtctac 660 atcctgtcca aggacgaggg tgggcgtcac accccgttct actcgaacta ccgcgcgcag 720 ttctacttcc gcaccaccga cgtcaccggc gtcatcacgc tgcccgaggg caccgagatg 780 gtcatgcccg gcgacaccac cgagatgtcg gtcgagctca tccagccgat cgccatggag 840 gagggcctcg gcttcgccat ccgcgagggt ggccgcaccg tgggctccgg c 891 160 891 DNA Mycobacterium tuberculosis 160 aacatgatca ccggcgccgc gcagatggac ggtgcgatcc tggtggtcgc cgccaccgac 60 ggcccgatgc cccagacccg cgagcacgtt ctgctggcgc gtcaagtggg tgtgccctac 120 atcctggtag cgctgaacaa ggccgacgca gtggacgacg aggagctgct cgaactcgtc 180 gagatggagg tccgcgagct gctggctgcc caggaattcg acgaggacgc cccggttgtg 240 cgggtctcgg cgctcaaggc gctcgagggt gacgcgaagt gggttgcctc tgtcgaggaa 300 ctgatgaacg cggtcgacga gtcgattccg gacccggtcc gcgagaccga caagccgttc 360 ctgatgccgg tcgaggacgt cttcaccatt accggccgcg gaaccgtggt caccggacgt 420 gtggagcgcg gcgtgatcaa cgtgaacgag gaagttgaga tcgtcggcat tcgcccatcg 480 accaccaaga ccaccgtcac cggtgtggag atgttccgca agctgctcga ccagggccag 540 gcgggcgaca acgttggttt gctgctgcgg ggcgtcaagc gcgaggacgt cgagcgtggc 600 caggttgtca ccaagcccgg caccaccacg ccgcacaccg agttcgaagg ccaggtctac 660 atcctgtcca aggacgaggg cggccggcac acgccgttct tcaacaacta ccgtccgcag 720 ttctacttcc gcaccaccga cgtgaccggt gtggtgacac tgccggaggg caccgagatg 780 gtgatgcccg gtgacaacac caacatctcg gtgaagttga tccagcccgt cgccatggac 840 gaaggtctgc gtttcgcgat ccgcgagggt ggccgcaccg tgggcgccgg c 891 161 891 DNA Mycoplasma genitalium 161 aatatgatca caggtgctgc acaaatggat ggagctattc tagttgtttc agcaactgat 60 agtgtgatgc cccaaacccg cgagcacatc ttacttgccc gccaagtagg ggttcctaaa 120 atggtagttt ttctaaacaa gtgtgatatt gctagtgatg aagaggtaca agaacttgtt 180 gctgaagaag tacgtgatct gttaacttcc tatggttttg atggtaagaa cactcctatt 240 atttatggct cagctttaaa agcattggaa ggtgatccaa agtgggaggc taagatccat 300 gatttgatta aagcagttga tgaatggatt ccaactccta cacgtgaagt agataaacct 360 ttcttattag caattgaaga tacgatgacc attactggta gaggtacagt tgttacagga 420 agagttgaaa gaggtgaact caaagtaggt caagaagttg aaattgttgg tttaaaacca 480 attagaaaag cagttgttac tggaattgaa atgttcaaaa aggaacttga ttcagcaatg 540 gctggtgaca atgctggggt attattacgt ggtgttgaac gtaaagaagt tgaaagaggt 600 caagttttag caaaaccagg ctctattaaa ccgcacaaga aatttaaagc tgagatctat 660 gctttaaaga aagaagaagg tggtagacac actggttttt taaacggtta ccgtcctcaa 720 ttctatttcc gtaccactga tgtaactggt tctattgctt tagctgaaaa tactgaaatg 780 gttctacctg gtgataatgc ttctattact gttgagttaa ttgctcctat cgcttgtgaa 840 aaaggtagta agttctcaat tcgtgaaggt ggtagaactg taggggcagg c 891 162 891 DNA Neisseria gonorrhoeae 162 aacatgatta ccggcgccgc acaaatggac ggtgcaatcc tggtatgttc tgctgccgac 60 ggccctatgc cgcaaacccg cgaacacatc ctgctggccc gtcaagtagg cgtaccttac 120 atcatcgtgt tcatgaacaa atgcgacatg gtcgacgatg ccgagctgtt ccaactggtt 180 gaaatggaaa tccgcgacct gctgtccagc tacgacttcc ccggcgacga ctgcccgatc 240 gtacaaggtt ccgcactgaa agccttggaa ggcgatgccg cttacgaaga aaaaatcttc 300 gaactggcta ccgcattgga cagatacatc ccgactcccg agcgtgccgt ggacaaacca 360 ttcctgctgc ctatcgaaga cgtgttctcc atttccggcc gcggtaccgt agtcaccggc 420 cgtgtagagc gaggtatcat ccacgttggt gacgagattg aaatcgtcgg tctgaaagaa 480 acccaaaaaa ccacctgtac cggcgttgaa atgttccgca aactgctgga cgaaggtcag 540 gcgggcgaca acgtaggcgt attgctgcgc ggtaccaaac gtgaagacgt agaacgcggt 600 caggtattgg ccaaacgggg tactatcact cctcacacca agttcaaagc agaagtgtac 660 gtattgagca aagaagaggg cggcccccat accccgtttt tcgccaacta ccgtccccaa 720 ttctacttcc gtaccactga cgtaaccggc acgattactt tggaaaaagg tgtggaaatg 780 gtaatgccgg gtgagaacgt aaccattact gtagaactga ttgcgcctat cgctatggaa 840 gaaggtctgc gctttgcgat tcgcgaaggc ggccgtaccg tgggtgccgg c 891 163 891 DNA Rickettsia prowazekii 163 aatatgataa ctggtgccgc tcagatggat ggtgctatat tagtagtttc tgctgctgat 60 ggtcctatgc ctcaaactag agaacatata ttactggcaa aacaggtagg tgtacctgct 120 atggtagtat ttttgaataa agtagatatg gtagatgatc ctgacctatt agaattagtt 180 gagatggaag taagagaatt attatcaaaa tatggtttcc ctggtaatga aatacctatt 240 attaaaggtt ctgcacttca agctttagaa ggaaaacctg aaggtgaaaa agctattaat 300 gagttaatga atgcagtaga tacgtatata cctcagccta tagagctaca agataaacct 360 tttttaatgc caatagagga tgtattttct atttcaggca gaggtaccgt tgtaactggt 420 agagtggagt caggcataat taaggtgggt gaagaaattg aaatagtagg tctaaaaaat 480 acgcaaaaaa cgacttgtac aggtgtagaa atgttcagaa aattacttga tgaaggacaa 540 tctggagata atgtcggtat attactacgt ggtacaaaaa gagaagaagt agaaagagga 600 caagtacttg caaaacctgg gagcataaaa ccgcatgata aatttgaagc tgaagtgtat 660 gtgcttagta aagaggaagg tggacgtcat accccattta ctaatgatta tcgcccacag 720 ttctatttta gaacaacaga tgttaccggc acaataaaat tgccttctga taagcagatg 780 gttatgcctg gagataatgc tactttttca gtagaattaa ttaagccgat tgctatgcaa 840 gaagggttaa aattctctat acgtgaaggt ggtagaacag taggagccgg t 891 164 891 DNA Salmonella typhimurium 164 aacatgatca ccggtgctgc tcagatggac ggcgcgatcc tggttgttgc tgcgactgac 60 ggcccgatgc cgcagacccg tgagcacatc ctgctgggtc gtcaggtagg cgttccgtac 120 atcatcgtgt tcctgaacaa atgcgacatg gttgatgacg aagagctgct ggaactggtt 180 gagatggaag ttcgcgaact gctgtctcag tacgacttcc cgggcgacga cactccgatc 240 gttcgtggtt ctgctctgaa agcgctggaa ggcgacgcag agtgggaagc gaaaatcatc 300 gaactggctg gcttcctgga ttcttatatt ccggaaccag agcgtgcgat tgacaagccg 360 ttcctgctgc cgatcgaaga cgtattctcc atctccggtc gtggtaccgt tgttaccggt 420 cgtgtagagc gcggtatcat caaagtgggc gaagaagttg aaatcgttgg tatcaaagag 480 actcagaagt ctacctgtac tggcgttgaa atgttccgca aactgctgga cgaaggccgt 540 gccggtgaga acgtaggtgt tctgctgcgt ggtatcaaac gtgaagaaat cgaacgtggt 600 caggtactgg ctaagccggg caccatcaag ccgcacacca agttcgaatc tgaagtgtac 660 attctgtcca aagatgaagg cggccgtcat actccgttct tcaaaggcta ccgtccgcag 720 ttctacttcc gtactactga cgtgactggt accatcgaac tgccggaagg cgtagagatg 780 gtaatgccgg gcgacaacat caaaatggtt gttaccctga tccacccgat cgcgatggac 840 gacggtctgc gtttcgcaat ccgtgaaggc ggccgtaccg ttggcgcggg c 891 165 881 DNA Shewanella putida 165 atgatcactg gtgctgcaca gatggacggc gcgattctgg tagtcgcttc aacagacggt 60 ccaatgccac agactcgtga gcacatcctg ctttctcgtc aggttggcgt accattcatc 120 atcgtattca tgaacaaatg tgacatggta gatgacgaag agctgttaga gctagttgag 180 atggaagtgc gtgaactgtt atcagaatac gatttcccag gtgatgactt accggtaatc 240 caaggttcag ctctgaaagc gctagaaggc gagccagagt gggaagcaaa aatccttgaa 300 ttagcagcgg cgctggattc ttacattcca gaaccacaac gtgacatcga taagccgttc 360 ctactgccaa tcgaagacgt attctcaatt tcaggccgtg gtacagtagt aacaggtcgt 420 gttgagcgtg gtattgtacg cgtaggcgac gaagttgaaa tcgttggtgt acgtgcgaca 480 actaagacaa cgtgtactgg tgtagaaatg ttccgtaaac tgcttgacga aggtcgtgca 540 ggtgagaact gtggtatttt gttacgtggt actaagcgtg atgacgtaga acgtggtcaa 600 gtattagcga agccaggttc aatcaaccca cacactactt ttgaatcaga agtttacgta 660 ctgtcaaaag aagaaggtgg tcgtcacacg ccattcttca aaggctaccg tccacagttc 720 tacttccgta caactgacgt aaccggtact atcgaactgc cagaaggcgt agagatggta 780 atgccaggcg ataacatcaa gatggtagtg acactgattt gcccaatcgc gatggacgaa 840 ggtttacgct tcgcaatccg tgaaggcggt cgtacagtgg t 881 166 897 DNA Stigmatella aurantiaca 166 aacatgatca cgggcgcggc gcagatggac ggagcgattc tggtggtgtc cgcggccgac 60 ggcccgatgc cccagacgcg tgagcacatc ctgctggcca ggcaggtggg cgtgccctac 120 atcgtcgtct tcctgaacaa ggtggacatg ctggacgatc cggagctgcg cgagctggtg 180 gagatggagg tgcgcgacct gctcaagaag tacgagttcc cgggcgacag catccccatc 240 atccctggca gcgcgctcaa ggcgctggag ggagacacca gcgacatcgg cgagggagcg 300 atcctgaagc tgatggcggc ggtggacgag tacatcccga cgccgcagcg tgcgacggac 360 aagccgttcc tgatgccggt ggaagacgtg ttctccatcg caggccgagg aacggtggcg 420 acgggccgag tggagcgcgg caagatcaag gtgggcgagg aagtggagat cgtggggatc 480 cgtccgacgc agaagacggt catcacgggg gtggagatgt tccgcaagct gctggacgag 540 ggcatggcgg gagacaacat cggagcgctg ctgcgaggcc tgaagcgcga ggacctggag 600 cgtgggcagg tgctggcgaa ctgggggagc atcaacccgc acacgaagtt caaggcgcag 660 gtgtacgtgc tgtcgaagga agagggaggg cggcacacgc cgttcttcaa gggataccgg 720 ccgcagttct acttccggac gacggacgtg accggaacgg tgaagctgcc ggacaacgtg 780 gagatggtga tgccgggaga caacatcgcc atcgaggtgg agctcattac tccggtcgcc 840 atggagaagg agctgccgtt cgccatccgt gagggtggcc gcacggtggg cgccggc 897 167 894 DNA Streptococcus pyogenes 167 aacatgatca ctggtgccgc tcaaatggac ggagctatcc ttgtagttgc ttcaactgat 60 ggaccaatgc cacaaactcg tgagcacatc cttctttcac gtcaggttgg tgttaaacac 120 cttatcgtgt tcatgaacaa agttgacctt gttgatgacg aagagttgct tgaattagtt 180 gagatggaaa ttcgtgacct tctttcagaa tacgatttcc caggtgatga ccttccagtt 240 atccaaggtt cagctcttaa agctcttgaa ggcgacacta aatttgaaga catcatcatg 300 gaattgatgg atactgttga ttcatacatt ccagaaccag aacgcgacac tgacaaacca 360 ttgcttcttc cagtcgaaga cgtattctca attacaggtc gtggtacagt tgcttcagga 420 cgtatcgacc gtggtactgt tcgtgtcaac gacgaaatcg aaatcgttgg tatcaaagaa 480 gaaactaaaa aagctgttgt tactggtgtt gaaatgttcc gtaaacaact tgacgaaggt 540 cttgcaggag acaacgtagg tatccttctt cgtggtgttc aacgtgacga aatcgaacgt 600 ggtcaagtta ttgctaaacc aagttcaatc aacccacaca ctaaattcaa aggtgaagta 660 tatatccttt ctaaagacga aggtggacgt cacactccat tcttcaacaa ctaccgtcca 720 caattctact tccgtacaac tgacgtaaca ggttcaatcg aacttccagc aggtacagaa 780 atggttatgc ctggtgataa cgtgacaatc aacgttgagt tgatccaccc aatcgccgta 840 gaacaaggta ctactttctc aatccgtgaa ggtggacgta ctgttggttc aggt 894 168 897 DNA Thiobacillus cuprinus 168 aacatgatca ccggtgcggc ccagatggac ggcgccatcc tggtcgtgtc cgccgccgac 60 ggccccatgc cccaaacccg cgagcacatc ctgctggcgc gtcaggtggg cgtgccctac 120 atcatcgtgt tcctcaacaa gtgcgacatg gtcgacgacg ccgagctgct cgaactcgtc 180 gagatggaag tgcgcgagct gctgtccaag tacgacttcc ccggtgacga cacccccatc 240 atcaagggct cggccaagct ggccctcgaa ggcgacaagg gcgaactggg cgaaggcgcc 300 attctcaagc tggccgaggc cctggacacc tacatcccca cgcccgagcg ggccgtcgac 360 ggcgcgttcc tcatgcccgt ggaagacgtg ttctccatct ccgggcgcgg cacggtggtc 420 accgggcgtg tggagcgcgg catcatcaag gtcggcgagg aaatcgagat tgtcggcctc 480 aagcccaccc tcaagaccac ctgcaccggc gtggaaatgt tcaggaagct gctcgaccag 540 ggccaggccg gcgacaacgt cggcatcttg ctgcgcggca ccaagcgcga ggaagtcgag 600 cgcggccagg tgctgtgcaa acccggctcg atcaagcccc acacccactt caccgccgag 660 gtgtacgtgc tgagcaagga cgagggcggc cgccacaccc ccttcttcaa caactaccgc 720 ccgcagttct acttccgcac caccgacgtc accggcgcca tcgaactgcc caaggacaag 780 gaaatggtca tgcccggcga taatgtgagc atcaccgtca agctcatcgc ccccatcgcc 840 atggaagaag gcctgcgctt cgccatccgc gaaggcggcc gcaccgtcgg cgccggc 897 169 894 DNA Treponema pallidum 169 aatatgatca cgggtgctgc gcagatggac ggtggtattc tcgtcgtgtc tgcgcctgac 60 ggcgttatgc cacagacgaa ggagcatctt ctgctcgccc gtcaggttgg tgttccctcc 120 atcattgttt ttttgaacaa ggttgatttg gttgatgatc ctgagttgct agagctggtg 180 gaagaagagg tgcgtgatgc gcttgctgga tatgggtttt cgcgtgagac gcctatcgtc 240 aaggggtctg cgtttaaagc tctgcaggat ggcgcttccc cggaggatgc agcttgtatt 300 gaggaactgc ttgcggccat ggattcctac tttgaagacc cagtgcgtga cgacgcaaga 360 cctttcttgc tctctatcga ggatgtgtac actatttctg ggcgtggtac cgttgtcacg 420 gggcgcatcg aatgtggggt aattagtctg aatgaagagg tcgagatcgt cgggattaag 480 cccactaaga aaacagtggt tactggcatt gagatgttta ataagttgct tgatcaggga 540 attgcaggtg ataacgtggg gctgcttttg cgcggggtgg ataaaaaaga ggttgagcgc 600 ggtcaggtgc tttctaagcc cggttctatt aagccacaca ccaagtttga ggcgcagatc 660 tacgtgctct ctaaggaaga gggtggccgt cacagtcctt tttttcaagg ttatcgtccg 720 cagttttatt ttagaactac tgacattacc ggtacgattt ctcttcctga aggggtagac 780 atggtgaagc cgggggataa caccaagatt ataggtgagc tcatccaccc gatagctatg 840 gacaagggtc tgaagcttgc gattcgtgaa ggggggcgca ctattgcttc tggt 894 170 891 DNA Ureaplasma urealyticum 170 aatatgatta caggggcagc acaaatggat ggagcaattt tagttattgc tgcatctgat 60 ggggttatgg ctcaaactaa agaacatatt ttattagcac gtcaagttgg tgttccaaaa 120 atcgttgttt tcttaaacaa atgtgatttc atgacagatc cagatatgca agatcttgtt 180 gaaatggaag ttcgtgaatt attatctaaa tatggatttg atggcgataa cacaccagtt 240 attcgtggtt caggtcttaa ggctttagaa ggagatccag tttgagaagc aaaaattgat 300 gaattaatgg acgcagttga ttcatgaatt ccattaccag aacgtagtac tgacaaacca 360 ttcttattag caattgaaga tgtattcaca atttcaggac gtggtacagt agtaactgga 420 cgtgttgaac gtggtgtatt aaaagttaat gatgaggttg aaattgttgg tctaaaagac 480 actcaaaaaa ctgttgttac aggaattgaa atgtttagaa aatcattaga tcaagctgaa 540 gctggtgata atgctggtat tttattacgt ggtattaaaa aagaagatgt tgaacgtggt 600 caagtacttg taaaaccagg atcaattaaa cctcaccgta cttttactgc taaagtttat 660 attcttaaaa aagaagaagg tggacgtcat acacctattg tttcaggata ccgtccacaa 720 ttctatttta gaacaacaga tgtaacaggt gctatttcat tacctgctgg tgttgatttg 780 gttatgccag gtgatgacgt tgaaatgact gtagaattaa ttgctccagt tgcgattgaa 840 gatggatcta aattctcaat ccgtgaaggt ggtaaaactg taggtcatgg t 891 171 909 DNA Wolinella succinogenes 171 aacatgatta caggtgctgc tcaaatggat ggcgcgattc ttgttgtttc tgcggcggat 60 ggccccatgc cccaaactag ggagcacatt cttctttctc gacaagtagg cgttccttac 120 atcgtggttt tcttgaacaa agaagatatg gttgatgacg ctgagcttct tgagcttgtt 180 gaaatggaag ttagagaact tcttagcaac tacgacttcc ctggagatga cactcctatc 240 gttgcaggtt ccgctcttaa agctcttgaa gaggctaacg accaggaaaa tgttggcgag 300 tggggcgaga aagtattgaa gcttatggct gaggttgacc gatatattcc tacgcctgag 360 cgagatgtgg ataagccttt ccttatgcct gttgaagacg tattctccat cgcgggtcgt 420 ggaaccgttg tgacaggaag aattgaaaga ggcgtggtta aagtcggtga cgaagtagaa 480 atcgttggta tccgaaacac acaaaaaaca accgtaactg gcgttgagat gttccgaaaa 540 gagctcgaca agggtgaggc gggtgacaac gttggtgttc ttttgagagg caccaagaaa 600 gaagatgttg agagaggtat ggttctttgt aaaataggtt ctatcactcc tcacactaac 660 tttgaaggtg aagtttacgt tctttccaaa gaggaaggcg gacgacacac tccattcttc 720 aatggatacc gacctcagtt ctatgttaga actacagacg ttaccggttc tatctctctt 780 cctgagggcg tagagatggt tatgcctggt gacaacgtta agatcaatgt tgagcttatc 840 gctcctgtag ccctcgaaga gggaacacga ttcgcgatcc gtgaaggtgg tcgaaccgtt 900 ggtgcgggt 909 172 26 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 172 tartcngtra angcytcnac rcacat 26 173 21 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 173 tctttagcag aacaggatga a 21 174 20 DNA Artificial Sequence Description of Artificial Sequence synthetic DNA 174 gaataattcc atatcctccg 20 

What is claimed is:
 1. A method using probes and/or amplification primers which are specific, ubiquitous and sensitive for determining the presence and/or amount of nucleic acids: from a bacterial antibiotic resistance gene selected from the group consisting of bla_(tem), bla_(shv) bla_(rob) bla_(oxa) blaZ, aadB, aacC1, aacC2, aacC3, aac6′-lla, aacA4, aad(6′), vanA, vanB, vanC, msrA, sata, aac(6′)-aph(2″), vat, vga, ermA, ermB, ermC, mecA, int and sul, and from specific bacterial and fungal species selected from the group consisting of Enterococcus faecium, Listeria monocytogenes, Neisseria meningitidis, Streptococcus agalactiae, Candida albicans, Enterococcus genus, Neisseria genus, Staphylococcus genus, Streptococcus genus and Candida genus, in any sample suspected of containing said bacterial and/or fungal nucleic acids, wherein each of said nucleic acid or variant or part thereof comprises a selected target region hybridizable with said probes or primers; said method comprising the following steps: contacting said sample with said probes or primers under uniform conditions of hybridization or amplification, and detecting the presence and/or amount of hybridized probes or amplified products as an indication of the presence and/or amount of said specific bacterial and/or fungal species or genus simultaneously with said bacterial antibiotic resistance genes.
 2. A method according to claim 1, which further makes use of probes and/or primers which are specific, ubiquitous and sensitive for simultaneously determining the presence and/or amount of nucleic acids from any bacterium or fungus.
 3. The method of claim 1, which is performed directly from a test sample.
 4. The method of claim 1, which is performed directly from a test sample consisting of a bacterial and/or fungal culture or suspension.
 5. The method of claim 1, wherein said nucleic acids are amplified by a method selected from the group consisting of: a) polymerase chain reaction (PCR), b) ligase chain reaction (LCR), c) nucleic acid sequence-based amplification (NASBA), d) self-sustained sequence replication (3SR), e) strand displacement amplification (SDA), f) branched DNA signal amplification (bDNA), g) transcription-mediated amplification (TMA), h) cycling probe technology (CPT), i) nested PCR, and j) multiplex PCR.
 6. The method of claim 6, wherein said nucleic acids are amplified by PCR.
 7. The method of claim 6, wherein the PCR protocol achieves within one hour under uniform amplification conditions the determination of the presence of said nucleic acids by performing for each amplification cycle an annealing step of thirty seconds at 45-55° C. and a denaturation step of only one second at 95° C. without any time specifically allowed to an elongation step.
 8. A method for the detection, identification and/or quantification of a microorganism selected from the group consisting of Enterococcus faecium, Listeria monocytogenes, Neisseria meningitidis, Staphylococcus saprophyticus, Streptococcus agalactiae, Candida albicans, Enterococcus species, Neisseria species, Staphylococcus species, Streptococcus species and Candida species, directly from a test sample or from bacterial and/or fungal cultures, which comprises the following steps: a) depositing and fixing on an inert support or leaving in solution the said microorganism DNA of the sample or of a substantially homogeneous population of said microorganism isolated from this sample, or inoculating said sample or said substantially homogeneous population of microorganism isolated from this sample on an inert support, and lysing in situ said inoculated sample or said isolated microorganism to release the said microorganism DNA, said microorganism DNA being made in a substantially single-stranded form; b) contacting said single-stranded DNA with a probe, said probe comprising at least one single-stranded nucleic acid which nucleotide sequence is selected from the group consisting of SEQ ID NOs: 26, 27, 28, 29, 30,120, 131 to 134, 31, 140 to 143, 32 to 36, 120 to 124, a sequence complementary thereof, a part thereof having at least 12 nucleotides in length, and a variant thereof, which specifically and ubiquitously anneals with strains or representatives of Enterococcus faecium, Listeria monocytogenes, Neisseria meningitidis, Staphylococcus saprophyticus, Streptococcus agalactiae, Candida albicans, Enterococcus species, Neisseria species, Staphylococcus species, Streptococcus species and Candida species, respectively, under conditions such that the nucleic acid of said probe can selectively hybridize with said microorganism DNA, whereby a hybridization complex is formed; and c) detecting the presence of said hybridization complex on said inert support or in said solution as an indication of the presence and/or amount of said microorganism, in said test sample.
 9. A method for detecting the presence and/or amount of a microorganism selected from the group consisting of Enterococcus faecium, Listeria monocytogenes, Neisseria meningitidis, Staphylococcus saprophyticus, Streptococcus agalactiae, Candida albicans, Enterococcus species, Neisseria species, Staphylococcus species, Streptococcus species and Candida species, in a test sample which comprises the following steps: a) treating said sample with an aqueous solution containing at least one pair of oligonucleotide primers having at least 12 nucleotides in length, one of said primers being capable of hybridizing selectively with one of the two complementary strands of said microorganism DNA that contains a target sequence, and the other of said primers being capable of hybridizing with the other of said strands so as to form an extension product which contains the target sequence as a template, said at least one pair of primers being chosen from a nucleotide sequence within the group consisting of SEQ ID NOs: 26, 27, 28, 29, 30, 120, 131 to 134, 31, 140 to 143, 32 to 36, 120 to 124, respectively with regard to said microorganism, a sequence complementary thereof, and a variant thereof; b) synthesizing an extension product of each of said primers, said extension product containing the target sequence, and amplifying said target sequence, if any, to a detectable level; and c) detecting the presence and/or amount of said amplified target sequence as an indication of the presence and/or amount of said microorganisms, in said test sample.
 10. The method of claim 9 wherein said pair of primers is defined in SEQ ID NOs: 1 and 2, 3 and 4, 5 and 6, 7 and 8, 9 and 10, 11 and 12, 13 and 14, 15 and 16, 17 to 20, 21 and 22, respectively, for each of Enterococcus faecium, Listeria monocytogenes, Neisseria meningitidis, Staphylococcus saprophyticus, Streptococcus agalactiae, Candida albicans, Enterococcus species, Neisseria species, Staphylococcus species and Streptococcus species.
 11. A method for detecting the presence and/or amount of any bacterium directly from a test sample or a bacterial culture, which comprises the following steps: a) depositing and fixing on an inert support or leaving in solution the bacterial DNA of the sample or of a substantially homogeneous population of bacteria isolated from this sample, or inoculating said sample or said substantially homogeneous population of bacteria isolated from this sample on an inert support, and lysing in situ said inoculated sample or isolated bacteria to release the bacterial DNA, said bacterial DNA being made in a substantially single-stranded form; b) contacting said single-stranded DNA with a probe, said probe comprising at least one single-stranded nucleic acid which nucleotide sequence is selected from the group consisting of SEQ ID NOs: 118, 119, 125 to 171, a sequence complementary thereof, a part thereof having at least 12 nucleotides in length, and a variant thereof, which specifically and ubiquitously anneals with strains or representatives of any bacterial species, under conditions such that the nucleic acid of said probe can selectively hybridize with said bacterial DNA, whereby a hybridization complex is formed; and c) detecting the presence of said hybridization complex on said inert support or in said solution as an indication of the presence and/or amount of any bacterium in said test sample.
 12. A method for detecting the presence and/or amount of any bacterium in a test sample which comprises the following steps: a) treating said sample with an aqueous solution containing at least one pair of oligonucleotide primers having at least 12 nucleotides in length, one of said primers being capable of hybridizing selectively with one of the two complementary strands of any bacterial DNA that contains a target sequence, and the other of said primers being capable of hybridizing with the other of said strands so as to form an extension product which contains the target sequence as a template, said at least one pair of primers being chosen from a nucleotide sequence within the group consisting of SEQ ID NO: 118, 119, 125 to 171, a sequence complementary thereof, and a variant thereof; b) synthesizing an extension product of each of said primers, said extension product containing the target sequence, and amplifying said target sequence, if any, to a detectable level; and c) detecting the presence and/or amount of said amplified target sequence as an indication of the presence and/or amount of any bacterium in said test sample.
 13. The method of claim 12, wherein said pair of primers is defined in SEQ ID NOs: 23 and
 24. 14. A method for obtaining tuf sequences from any bacterium directly from a test sample or a bacterial culture, which comprises the following steps: a) treating said sample with an aqueous solution containing a pair of primers having a sequence selected within the nucleotide sequences defined in SEQ ID NOs: 107 and 108, a part thereof having at least 12 nucleotides in length, a sequence complementary thereof, and a variant thereof, one of said primers being capable of hybridizing selectively with one of the two complementary strands of said bacterial tuf gene that contains a target sequence, and the other of said primers being capable of hybridizing with the other of said strands so as to form an extension product which contains the target sequence as a template; b) synthesizing an extension product of each of said primers, said extension product containing the target sequence, and amplifying said target sequence, if any, to a detectable level; and c) detecting the presence and/or amount of said amplified target sequence; and d) determining the nucleotide sequence of the said amplified target sequence by using any DNA sequencing method.
 15. A method for detecting the presence and/or amount of any fungus directly from a test sample or a fungal culture, which comprises the following steps: a) depositing and fixing on an inert support or leaving in solution the fungal DNA of the sample or of a substantially homogeneous population of fungi isolated from this sample, or inoculating said sample or said substantially homogeneous population of fungi isolated from this sample on an inert support, and lysing in situ said inoculated sample or isolated fungi to release the fungal DNA, said fungal DNA being made in a substantially single-stranded form; b) contacting said single-stranded DNA with a probe, said probe comprising at least one single-stranded nucleotide sequence selected from the group consisting of SEQ ID NOs: 120 to 124, a sequence complementary thereof, a part thereof having at least 12 nucleotides in length, and a variant thereof, which specifically and ubiquitously anneals with strains or representatives of any fungus, under conditions such that the nucleic acid of said probe can selectively hybridize with said fungal DNA, whereby a hybridization complex is formed; and c) detecting the presence of said hybridization complex on said inert support or in said solution as an indication of the presence and/or amount of any fungus in said test sample.
 16. A method for detecting the presence and/or amount of any fungus in a test sample which comprises the following steps: a) treating said sample with an aqueous solution containing at least one pair of oligonucleotide primers having at least 12 nucleotides in length, one of said primers being capable of hybridizing selectively with one of the two complementary strands of any fungal DNA that contains a target sequence, and the other of said primers being capable of hybridizing with the other of said strands so as to form an extension product which contains the target sequence as a template, said at least one pair of primers being chosen from a nucleotide sequence within the group consisting of SEQ ID NOs: 120 to 124, a sequence complementary thereof, and a variant thereof; b) synthesizing an extension product of each of said primers, said extension product containing the target sequence, and amplifying said target sequence, if any, to a detectable level; and c) detecting the presence and/or amount of said amplified target sequence as an indication of the presence and/or amount of any fungus in said test sample.
 17. A method for obtaining tuf sequences from any fungus directly from a test sample or a fungal culture, which comprises the following steps: a) treating said sample with an aqueous solution containing a pair of primers having a sequence selected within the nucleotide sequence defined in SEQ ID NOs: 109 and 172, a part thereof having at least 12 nucleotides in length, a sequence complementary thereof, and a variant thereof, one of said primers being capable of hybridizing selectively with one of the two complementary strands of said fungal tuf gene that contains a target sequence, and the other of said primers being capable of hybridizing with the other of said strands so as to form an extension product which contains the target sequence as a template; b) synthesizing an extension product of each of said primers, said extension product containing the target sequence, and amplifying said target sequence, if any, to a detectable level; and c) detecting the presence and/or amount of said amplified target sequence; and d) determining the nucleotide sequence of the said amplified target sequence by using any DNA sequencing method.
 18. A method as defined in any one of claims 1 to 8, which comprises the evaluation of the presence of a bacterial resistance mediated by a bacterial antibiotic resistance gene selected from the group consisting of bla_(oxa), blaZ, aac6′-lla, ermA, ermB, ermC, vanB, vanC, directly from a test sample or a bacterial culture, which comprises the following steps: a) depositing and fixing on an inert support or leaving in solution the bacterial DNA of the sample or of a substantially homogeneous population of bacteria isolated from this sample, or inoculating said sample or said substantially homogeneous population of bacteria isolated from this sample on an inert support, and lysing in situ said inoculated sample or isolated bacteria to release the bacterial DNA, said bacterial DNA being made in a substantially single-stranded form; b) contacting said single-stranded DNA with a probe, said probe comprising at least one single-stranded nucleotide sequence having at least 12 nucleotide in length is selected from the group consisting of SEQ ID NOs: 110, 111, 112, 113, 114 115, 116, 117, a sequence complementary thereof, and a variant thereof, which specifically hybridizes with said bacterial antibiotic resistance gene, respectively; and c) detecting the presence of a hybridization complex as an indication of a bacterial resistance mediated by said one of said bacterial antibiotic resistance genes.
 19. A method as defined in any one of claims 1 to 7, 9 and 10, which comprises the evaluation of the presence of a bacterial resistance mediated by a bacterial antibiotic resistance gene selected from the group consisting of bla_(oxa), blaZ, aac6′-lla, ermA, ermB, ermC, vanB, vanC, directly from a test sample or a bacterial culture, which comprises the following steps: a) treating said sample with an aqueous solution containing at least one pair of primers having at least 12 nucleotides in length, one of said primers being capable of hybridizing selectively with one of the two complementary strands of said bacterial antibiotic resistance gene that contains a target sequence, and the other of said primers being capable of hybridizing with the other of said strands so as to form an extension product which contains the target sequence as a template, said at least one pair of primers being chosen from a nucleotide sequence within the group consisting of SEQ ID NOs: 110, 111, 112, 113, 114, 115, 116, 117, respectively with regard to said bacterial antibiotic resistance gene, a sequence complementary thereof, and a variant thereof; b) synthesizing an extension product of each of said primers, said extension product containing the target sequence, and amplifying said target sequence, if any, to a detectable level; and c) detecting the presence and/or amount of said amplified target sequence as an indication of a bacterial resistance mediated by one of said bacterial antibiotic resistance genes.
 20. A method as defined in any one of claims 1 to 7, 9 and 10, which comprises the evaluation of the presence of a bacterial resistance gene selected from the group consisting of bla_(tem), bla_(shv), bla_(rob), bla_(oxa), blaZ, aadB, aacC1, aacC2, aacC3, aac6′-lla, aacA4, aad(6′), vanA, vanB, vanC, msrA, satA, aac(6′)-aph(2″), vat, vga, ermA, ermB, ermC, mecA, int and sul directly from a test sample or a bacterial culture, which comprises the following steps: a) treating said sample with an aqueous solution containing at least one pair of primers having a sequence selected in the group consisting of SEQ ID NOs: 37 to 40, 41 to 44, 45 to 48, 49 and 50, 51 and 52, 53 and 54, 55 and 56, 57 and 58, 59 to 60, 61 to 64, 65 and 66, 173 and 174, 67 to 70, 71 to 74, 75 and 76, 77 to 80, 81 and 82, 83 to 86, 87 and 88, 89 and 90, 91 and 92, 93 and 94, 95 and 96, 97 and 98, 99 to 102, 103 to 106, a part thereof having at least 12 nucleotides in length, a sequence complementary thereof, a variant thereof, and mixtures thereof, one of said primers of said pair being capable of hybridizing selectively with one of the two complementary strands of its respective bacterial antibiotic resistance gene that contains a target sequence, and the other of said primers of said pairs being capable of hybridizing with the other of said strands so as to form an extension product which contains the target sequence as a template; b) synthesizing an extension product of each of said primers, said extension product containing the target sequence, and amplifying said target sequence, if any, to a detectable level; and c) detecting the presence and/or amount of said amplified target sequence as an indication of a bacterial resistance mediated by one of said bacterial antibiotic resistance genes.
 21. A nucleic acid having the nucleotide sequence of any one of SEQ ID NOs: 26 to 36, 110 to 117, a part thereof, a sequence complementary thereof, and variant thereof which, when in single-stranded form, ubiquitously and specifically hybridizes with a target bacterial or fungal DNA as a probe or as a primer.
 22. An oligonucleotide having the nucleotide sequence of any one of SEQ ID NOs: 1 to 25, 37 to 71, 73 to 109 and 172 to 174, a part thereof, a sequence complementary thereof, and variant thereof, which ubiquitously and specifically hybridizes with a target bacterial or fungal DNA as a probe or as a primer.
 23. A recombinant plasmid comprising a nucleic acid as defined in claim
 22. 24. A recombinant host which has been transformed by a recombinant plasmid according to claim
 23. 25. A recombinant host according to claim 24 wherein said host is Escherichia coli.
 26. A diagnostic kit for the detection and/or quantification of the nucleic acids of any combination of the microbial species and/or genera selected from the group consisting of Enterococcus faecium, Listeria monocytogenes, Neisseria meningitidis, Staphylococcus saprophyticus, Streptococcus agalactiae, Candida albicans, Enterococcus species, Neisseria species, Staphylococcus species, Streptococcus species and Candida species, comprising any suitable combination of probes of at least 12 nucleotides in length selected from the group consisting of SEQ ID NOs: 26 to 36, 120 to 124, 131 to 134, 140 to 143, sequences complementary thereof, and variants thereof.
 27. A diagnostic kit for the detection and/or quantification of the nucleic acids of any combination of the microbial species and/or genera selected from the group consisting of Enterococcus faecium, Listeria monocytogenes, Neisseria meningitidis, Staphylococcus saprophyticus, Streptococcus agalactiae, Candida albicans, Enterococcus species, Neisseria species, Staphylococcus species, Streptococcus species and Candida species, comprising any suitable combination of primers of at least 12 nucleotides in length selected from the group consisting of SEQ ID NOs: 26 to 36, 120 to 124, 131 to 134, 140 to 143, sequences complementary thereof, and variants thereof.
 28. A diagnostic kit for the detection and/or quantification of the nucleic acids of any combination of the microbial species and/or genera selected from the group consisting of Enterococcus faecium, Listeria monocytogenes, Neisseria meningitidis, Staphylococcus saprophyticus, Streptococcus agalactiae, Candida albicans, Enterococcus species, Neisseria species, Staphylococcus species and Streptococcus species, comprising any suitable combination of primers selected from the group consisting of SEQ ID NOs: 1 to 22, parts thereof having at least 12 nucleotides in length, sequences complementary thereof, and variants thereof.
 29. A diagnostic kit for the detection and/or quantification of the nucleic acids of any combination of the bacterial resistance genes selected from the group consisting of bla_(oxa), blaZ, aac6′-lla, ermA, ermB, ermC, vanC, comprising any suitable combination of probes of at least 12 nucleotides in length selected from the group consisting of SEQ ID NOs: 110 to 115 and 117, sequences complementary thereof, and variants thereof.
 30. A diagnostic kit for the detection and/or quantification of the nucleic acids of any combination of the bacterial resistance genes selected from the group consisting of bla_(oxa), blaZ, aac6′-lla, ermA, ermB, ermC, vanC, comprising any suitable combination of primers of at least 12 nucleotides in length selected from the group consisting of SEQ ID NOs: 110 to 115 and 117, sequences complementary thereof, and variants thereof.
 31. A diagnostic kit for the detection and/or quantification of the nucleic acids of any bacterium and/or fungus, comprising any combination of probes of at least 12 nucleotides in length selected upon alignment of conserved nucleotides of at least two sequences of the group consisting of SEQ ID NOs: 118 to 171, sequences complementary thereof, and variants thereof.
 32. A diagnostic kit for the detection and/or quantification of the nucleic acids of any bacterium and/or fungus, comprising any suitable combination of primers of at least 12 nucleotides in length selected upon alignment of conserved nucleotides of at least two sequences the group consisting of SEQ ID NOs: 118 to 171, sequences complementary thereof, and variants thereof.
 33. A diagnostic kit for the detection and/or quantification of the nucleic acids of any bacterium, comprising a pair of primers having a sequence selected within the nucleotide sequence defined in SEQ ID NOs: 23 and 24, parts thereof having at least 12 nucleotides in length, sequences complementary thereof, and variants thereof.
 34. A diagnostic kit, as defined in claim 26, further comprising any combination of probes of at least 12 nucleotides in length selected within a nucleotide sequence from the group consisting of SEQ ID NOs: 118 to 171, sequences complementary thereof, and variants thereof, for the simultaneous detection and/or quantification of nucleic acids of any bacterium and/or fungus.
 35. A diagnostic kit, as defined in claim 27, further comprising any suitable combination of primers of at least 12 nucleotides in length selected within a nucleotide sequence from the group consisting of SEQ ID NOs: 118 to 171, sequences complementary thereof, and variants thereof, for the simultaneous detection and/or quantification of nucleic acids of any bacterium and/or fungus.
 36. A diagnostic kit, as defined in claim 28, further comprising a pair of primers having a sequence selected within the nucleotide sequence defined in SEQ ID NOs: 23 and 24, parts thereof having at least 12 nucleotides in length, sequences complementary thereof, and variants thereof, for the simultaneous detection and/or quantification of nucleic acids of any bacterium.
 37. A diagnostic kit, as defined in claim 26, further comprising any combination of probes of at least 12 nucleotides in length selected within a nucleotide sequence from the group consisting of SEQ ID NOs: 110 to 117, sequences complementary thereof, and variants thereof, for the simultaneous detection and/or quantification of nucleic acids of any bacterial antibiotic resistance gene selected from the group consisting of bla_(oxa), blaZ, aac6′-lla, ermA, ermB, ermC, vanB, vanC.
 38. A diagnostic kit, as defined in claim 27, further comprising any suitable combination of primers of at least 12 nucleotides in length selected within a nucleotide sequence from the group consisting of SEQ ID NOs: 110 to 117, sequences complementary thereof, and variants thereof, for the simultaneous detection and/or quantification of nucleic acids of any bacterial antibiotic resistance gene selected from the group consisting of bla_(oxa), blaZ, aac6′-lla, ermA, ermB, ermC, vanB, vanC.
 39. A diagnostic kit, as defined in claim 28, further comprising any suitable combination of primers of at least 12 nucleotides in length selected within a nucleotide sequence from the group consisting of SEQ ID NOs: 37 to 106, 173 and 174, sequences complementary thereof, and variants thereof, for the simultaneous detection and/or quantification of nucleic acids of any bacterial antibiotic resistance gene selected from the group consisting of bla_(tem), bla_(rob), bla_(shv), bla_(oxa), blaZ, aadB, aacC1, aacC2, aacC3, aacA4, aac6′-lla, aad(6′), ermA, ermB, ermC, mecA, vanA, vanB, vanC, satA, aac(6′)-aph(2″), vat, vga, msrA, sul and int.
 40. A diagnostic kit, as defined in claim 29, further comprising any combination of probes of at least 12 nucleotides in length selected within a nucleotide sequence from the group consisting of SEQ ID NOs: 116 and 118 to 171, sequences complementary thereof, and variants thereof, for the simultaneous detection and/or quantification of nucleic acids of vancomycin B gene and of any bacterium and/or fungus, respectively.
 41. A diagnostic kit, as defined in claim 30, further comprising any suitable combination of primers of at least 12 nucleotides in length selected within a nucleotide sequence from the group consisting of SEQ ID NOs: 116 and 118 to 171, sequences complementary thereof, and variants thereof, for the simultaneous detection and/or quantification of nucleic acids of vancomycin B gene and of any bacterium and/or fungus, respectively.
 42. A diagnostic kit for the detection and/or quantification of the nucleic acids of any bacterium and/or fungus, comprising any suitable combination of primers of at least 12 nucleotides in length selected upon alignment of conserved nucleotides of at least two sequences the group consisting of SEQ ID NOs: 118 to 171, sequences complementary thereof, and variants thereof and further comprising a pair of primers having a sequence selected within the nucleotide sequence defined in SEQ ID NOs: 23 and 24, parts thereof having at least 12 nucleotides in length, sequences complementary thereof, and variants thereof, for the simultaneous detection and/or quantification of nucleic acids of any bacterium.
 43. A diagnostic kit, as defined in claim 37, further comprising any combination of probes of at least 12 nucleotides in length selected within a nucleotide sequence from the group consisting of SEQ ID NOs: 118 to 171, sequences complementary thereof, and variants thereof, for the simultaneous detection and/or quantification of nucleic acids of any bacterium and/or fungus.
 44. A diagnostic kit, as defined in claim 38, further comprising any suitable combination of primers of at least 12 nucleotides in length selected within a nucleotide sequence from the group consisting of SEQ ID NOs: 118 to 171, sequences complementary thereof, and variants thereof, for the simultaneous detection and/or quantification of nucleic acids of any bacterium and/or fungus.
 45. A diagnostic kit, as defined in claim 39, further comprising a pair of primers having a sequence selected within the nucleotide sequence defined in SEQ ID NOs: 23 and 24, parts thereof having at least 12 nucleotides in length, sequences complementary thereof, and variants thereof, for the simultaneous detection and/or quantification of nucleic acids of any bacterium. 